Hello,

Sorry for being late, again, but please find the tool attached.

Here is my last pull: 5743:720455407d1c

Stuff changed in the file but in the end I had to make the same modification again (change true to false) since it didn't work anymore.

Best,
L-A



Le 15/06/2011 09:56, Louise-Amélie Schmitt a écrit :
Hi, and sorry for the late reply

Here is the last pull: 5355:50e249442c5a

I'll try to be as concise as I can but I can send you the whole file if you need it. It's not completely done yet though.

This is a tool that produces a HTML file containing the results of various quality assessment programs. To trigger or block the execution of a specific program, I use checkboxes in the form, like this:
<param name="SQA" type="boolean" label="Run SolexaQA" checked="true" />

Then, I use the <configfile name="script"> tags to define a shell script that will be modified with cheetah tests on the checkboxes.

Then the final script is sent to another shell script that will check its existence and launch it:
<command interpreter='sh'>all_QA.sh $script </command>

As you can see, the checkboxes are checked by default. But before the change I mentioned is my last email, un-checking them didn't have any effect whatsoever. The following test, for instance, was always true:
#if $SQA.value == True

Moreover, even if I un-checked the checkboxes and ran the tool, then clicked the re-run button in the result in my history, all of them were checked in the form that appears, as if I never un-checked them.

Now, the state of the checkboxes is respected and I can properly choose what to run in my tool.

Hope that helps.
L-A


Le 08/06/2011 20:54, Jennifer Jackson a écrit :
Hi L-A,

Could you describe a use case (which tool/from, what options/input)? If you know the last pull # for your local install, that would also be helpful for us to know.

Best,

Jen
Galaxy team

On 6/6/11 2:15 AM, Louise-Amélie Schmitt wrote:
Hi,

Since I haven't updated Galaxy for a while now I don't know if it was
actually fixed but I had issues with my default-selected checkboxes:

When I deselected them, the value sent in the query remained as if they
were still selected. Even when I re-ran the job, all the checkboxes were
selected as if I never deselected them.

Therefore, in lib/galaxy/web/form_builder.py

I changed:
105 return '<input type="checkbox" id="%s" name="%s"
value="true"%s%s><input type="hidden" name="%s%s" value="true"%s>' \

for:
105 return '<input type="checkbox" id="%s" name="%s"
value="true"%s%s><input type="hidden" name="%s%s" value="false"%s>' \

And it works fine now :)

Cheers,
L-A
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<tool id="all_QA" name="QA Bundle" description="performs multiple QA">
	<command interpreter='sh'>all_QA.sh $script </command>
	<inputs>

	        <param name="input" type="data" label="Input file" format="fastq,fastqillumina,sam,export,bam" checked="true" />
                

		<param name="R" type="boolean" label="Run R QA (runs only on export files)" checked="true" />


		<param name="HTSeq" type="boolean" label="Run HTSeq QA" checked="true" />


		<param name="C" type="boolean" label="Run baseQual (work only with fastq files)" checked="true" />

		<param name="SQA" type="boolean" label="Run SolexaQA" checked="true" />

		<param type="select" name="SQA_cutoff" label="&#60;span style=&#34;font-weight:normal;&#34;&#62;Cutoff (phred value at which base-calling error is considered too high)&#60;/span&#62;" help="">
	   		<option value="10">10 (90%)</option>
	   		<option value="13" selected="true">13 (95%)</option>
	   		<option value="20">20 (99%)</option>
	   		<option value="30">30 (99.9%)</option>
	   		<option value="40">40 (99.99%)</option>
		</param>
		<param type="select" name="SQA_variance" label="&#60;span style=&#34;font-weight:normal;&#34;&#62;Calculate variance statistics&#60;/span&#62;" display="radio" help="">
	   		<option value="" selected="true">No thanks</option>
	   		<option value="-v">Yes please</option>
		</param>
		<param type="select" name="SQA_minmax" label="&#60;span style=&#34;font-weight:normal;&#34;&#62;Calculate minimum and maximum error probabilities for each read position of each tile&#60;/span&#62;" display="radio" help="">
	   		<option value="" selected="true">No thanks</option>
	   		<option value="-m">Yes please</option>
		</param>
		<param name="SQA_sample" size="6" type="integer" value="10000" label="&#60;span style=&#34;font-weight:normal;&#34;&#62;Number of sequences to be sampled per tile for satistic estimates&#60;/span&#62;" help="" />
		
		
		<param name="CovE" type="boolean" label="Run Coverage Estimation" checked="true" />
		<param type="select" name="window" label="&#60;span style=&#34;font-weight:normal;&#34;&#62;Windows size for &#60;b&#62;Coverage&#60;/b&#62;, &#60;b&#62;Data On Target&#60;/b&#62; and &#60;b&#62;GC content&#60;/b&#62;&#60;/span&#62;" help="">
	   		<option value="10000" selected="true">10,000</option>
	   		<option value="1000">1,000</option>
	   		<option value="100">100</option>
		</param>
		
                <param name="DoT" type="boolean" label="Run Data on Target" checked="true" />
                <param name="DoT_chr" size="2" type="integer" value="1" label="&#60;span style=&#34;font-weight:normal;&#34;&#62;Target chromosome number&#60;/span&#62;" help="" />
                <param name="DoT_start" size="6" type="integer" value="0" label="&#60;span style=&#34;font-weight:normal;&#34;&#62;Target start position&#60;/span&#62;" help="" />
                <param name="DoT_end" size="6" type="integer" value="0" label="&#60;span style=&#34;font-weight:normal;&#34;&#62;Target end position&#60;/span&#62;" help="" />
                
		<param name="GC" type="boolean" label="Run GC content" checked="true" />
                
                <param name="MAP" type="boolean" label="Run Mappability" checked="true" />
                
                <param name="RU" type="boolean" label="Run redundancy/uniqueness" checked="true" />
                
		<param name="yield" type="boolean" label="Run yield" checked="true" />
		
		<param name="scatterplot" type="boolean" label="Run +/- scatter plot" checked="true" />
		<param type="select" name="bin_size" label="&#60;span style=&#34;font-weight:normal;&#34;&#62;Windows (bin) size for the plot&#60;/span&#62;" help="">
	   		<option value="10000" selected="true">10,000</option>
	   		<option value="1000">1,000</option>
	   		<option value="100">100</option>
		</param>
                
	</inputs>
	<configfiles>
	  <configfile name="script">
		## define function to test the exit of command line
		checkStatus(){	
		    if [ $? -ne 0 ]; then
			echo
			if [ -z $1 ]; then
			    echo "ERROR: Exiting as the process failed unexpectedly."
			else
			    echo "ERROR: $1."
			fi
			exit 1;	
		    fi
		}
		## Create the folder containing all data
		mkdir $output_html.extra_files_path

		## Begin the writting of the html report
		echo '&#60;html&#62;&#60;head&#62;'>>$output_html

		## Add QA.css style if R qa is active
		#if $R.value == True and $input.ext == "export"	
			echo '&#60;meta http-equiv="Content-Type"content="text/html; charset=utf-8"&#62;&#60;/meta&#62;'>>$output_html
			echo '&#60;link rel="stylesheet" type="text/css" href="QA.css" /&#62;'>>$output_html
		#end if
		
		## Coverage preprocessing if needed (creates the coverage file for the dataset and window size)
		#if ($CovE.value == True or $DoT.value == True or $GC.value == True) and ($input.ext == "sam" or $input.ext == "bam")
		        cov_file_available='False'
		        cov_file_name=/tmp/\$(basename ${input.file_name})_${window}.cov
		        if test -s \$cov_file_name
		        then
		                cov_file_available='True'
		        else
                                seq_path=`python ${ os.getcwd() }/${ $__app__.config.tool_path }/EMBL_tools/getRefSeq.py ${input.metadata.dbkey} "sam_fa_indices.loc" ${GALAXY_DATA_INDEX_DIR}`
			        ${ os.getcwd() }/${ $__app__.config.tool_path }/EMBL_tools/cov -g \$seq_path -w $window -o $window ${input.file_name} >\$cov_file_name 2>/dev/null
			        checkStatus "Coverage preprocessing failed."
			        if test -s \$cov_file_name
		                then
		                        cov_file_available='True'
		                fi
			fi
		#end if
		
		## GC preprocessing if needed (creates the GC content file for the reference genome and window size)
		#if $GC.value == True and ($input.ext == "sam" or $input.ext == "bam")
		        gc_file_available='False'
		        gc_file_name=${ os.getcwd() }/tool-data/gc_content/${input.metadata.dbkey}_${window}.gc
		        if test -s \$gc_file_name
		        then
		                gc_file_available='True'
		        else
                                seq_path=`python ${ os.getcwd() }/${ $__app__.config.tool_path }/EMBL_tools/getRefSeq.py ${input.metadata.dbkey} "sam_fa_indices.loc" ${GALAXY_DATA_INDEX_DIR}`
                                echo \$gc_file_name >> /g/funcgen/galaxy/erreurs.txt
                                echo \$seq_path >> /g/funcgen/galaxy/erreurs.txt
                                touch \$gc_file_name
			        perl ${ os.getcwd() }/${ $__app__.config.tool_path }/EMBL_tools/gcContentWindow.pl \$seq_path $window $window >\$gc_file_name 2>>/g/funcgen/galaxy/erreurs.txt
			        checkStatus "GC preprocessing failed."
			        if test -s \$gc_file_name
		                then
		                        gc_file_available='True'
		                fi
			fi
		#end if

		echo '&#60;/head&#62;&#60;body&#62;&#60;h1&#62;${output_html.name}&#60;/h1&#62;'>>$output_html
		
		## R process 
		#if $R.value == True and $input.ext == "export"
			mkdir $output_html.extra_files_path/symbolic_tmp
			ln -s $input.file_name $output_html.extra_files_path/symbolic_tmp/
			#set $directory = $output_html.extra_files_path + '/symbolic_tmp/'
			

			
			## run R [$datasets = input file; $R.type_R = type; $output_html.extra_files_path = output dir]
			R --vanilla --min-nsize=20M --min-vsize=12G --args ${directory} SolexaExport $output_html.extra_files_path/ &#60;${ os.getcwd() }/${ $__app__.config.tool_path }/EMBL_tools/qa.R 2>&#38;1 /dev/null
			checkStatus "R processing failed."
			

			
			##clean extra file
			rm $output_html.extra_files_path/symbolic_tmp/*
			rmdir $output_html.extra_files_path/symbolic_tmp
			## move every thing to build the report
			mv $output_html.extra_files_path/qa/index.html $output_html.extra_files_path/
			mv $output_html.extra_files_path/qa/QA.css $output_html.extra_files_path/
			mv $output_html.extra_files_path/qa/image/* $output_html.extra_files_path
			rm -r $output_html.extra_files_path/qa
			replace \"./image/ \" -- $output_html.extra_files_path/index.html
			

			
			echo '&#60;h2&#62; R report &#60;/h2&#62;' >>$output_html
			sed '1,10d' $output_html.extra_files_path/index.html |sed '214,215d' >>$output_html	
		#end if

		## HTSeq process
		#if $HTSeq.value == True and ($input.ext == "fastq" or $input.ext == "fastqsolexa" or $input.ext == "fastqsanger" or $input.ext == "fastqillumina" or $input.ext == "sam" or $input.ext == "bam")
			#if $input.ext == "export"
				/g/steinmetz/collaboration/software/CentOS5/bin/htseq-qa -t solexa-export -o $output_html.extra_files_path/htseq.pdf ${input.file_name}
                        #else if  $input.ext == "fastqsolexa" or $input.ext == "fastqillumina"
				/g/steinmetz/collaboration/software/CentOS5/bin/htseq-qa -t solexa-fastq -o $output_html.extra_files_path/htseq.pdf ${input.file_name}
			#else if $input.ext == "sam"
				/g/steinmetz/collaboration/software/CentOS5/bin/htseq-qa -t sam -o $output_html.extra_files_path/htseq.pdf ${input.file_name}
			#else if $input.ext == "bam"
				/g/steinmetz/collaboration/software/CentOS5/bin/htseq-qa -t bam -o $output_html.extra_files_path/htseq.pdf ${input.file_name}
	                #else if $input.ext == "fastqsanger" or $input.ext == "fastq"
				/g/steinmetz/collaboration/software/CentOS5/bin/htseq-qa -t fastq -o $output_html.extra_files_path/htseq.pdf ${input.file_name}
			#else
				echo '&#60;p&#62;HTSeq: unknown file type&#60;/p&#62;' >>$output_html
				##python -m HTSeq.scripts.qa -t fastq -o $output_html.extra_files_path/htseq.pdf ${input.file_name}
				##/g/steinmetz/collaboration/software/CentOS5/bin/htseq-qa -t fastq -o $output_html.extra_files_path/htseq.pdf ${input.file_name}
			#end if
			##echo "$output_html.extra_files_path/htseq.pdf"
			checkStatus "HTSeq processing failed."
			cd $output_html.extra_files_path/
			ls
			convert htseq.pdf htseq.jpg
			checkStatus "convert processing failed."
			cd -
			echo '&#60;hr/&#62;&#60;h2&#62;HTSeq report &#60;/h2&#62;'>>$output_html
			echo "&#60;p&#62;&#60;a href="htseq.pdf"&#62;htseq.pdf&#60;/a&#62;&#60;/p&#62;">>$output_html
			echo '&#60;img src="htseq.jpg"&#62;'>>$output_html
			echo '${input.file_name}' >> $output_html
		#end if


		## BaseQual process
		#if $C.value == True and ($input.ext == "fastq" or $input.ext == "fastqsanger" or $input.ext == "fastqsolexa" or $input.ext == "fastqillumina")
			baseQual ${input.file_name} > $output_html.extra_files_path/C_report.txt
			checkStatus "C processing failed."
			## Create table in the HTML report
			echo '&#60;hr/&#62;&#60;h2&#62;baseQual report &#60;/h2&#62;' >> $output_html
			##echo '&#60;table border="border"&#62;' &#62;&#62; $output_html
			##echo "&#60;tr&#62;&#60;td&#62;Base&#60;/td&#62; &#60;td&#62;Quality value&#60;/td&#62;&#60;/tr&#62;" &#62;&#62; $output_html
				
			## add result in the table
			sh ${ os.getcwd() }/${ $__app__.config.tool_path }/EMBL_tools/all_QA_C.sh $output_html.extra_files_path/C_report.txt $output_html
				
			echo '&#60;/table&#62;' &#62;&#62; $output_html 
			rm $output_html.extra_files_path/C_report.txt
		#end if
		
		## SolexaQA process
		#if $SQA.value == True and ($input.ext == "fastqillumina" or $input.ext == "fastqsolexa")
			cd $output_html.extra_files_path/
			echo "command: sh SolexaQA.sh -h ${SQA_cutoff} ${SQA_variance} ${SQA_minmax} -s ${SQA_sample} ${input.file_name}"
			sh SolexaQA.sh -h ${SQA_cutoff} ${SQA_variance} ${SQA_minmax} -s ${SQA_sample} ${input.file_name}
			checkStatus "SolexaQA processing failed."
			convert `basename ${input.file_name}`.quality.pdf  `basename ${input.file_name}`.quality.jpg 
			convert `basename ${input.file_name}`.segments.hist.pdf `basename ${input.file_name}`.segments.hist.jpg
			checkStatus "SolexaQA PDF output convert processing failed."
			cd -
				
			echo '&#60;hr/&#62;&#60;h2&#62;SolexaQA report &#60;/h2&#62;'>>$output_html
				
			echo "&#60;p&#62;&#60;h2&#62;Heat map:&#60;/h2&#62;&#60;/p&#62;">>$output_html
			echo '&#60;img src="'>>$output_html
			basename ${input.file_name} >>$output_html
			echo '.png"&#62;'>>$output_html
				
				
			echo "&#60;p&#62;&#60;h2&#62;Distribution of mean quality:&#60;/h2&#62;&#60;/p&#62;">>$output_html
			echo '&#60;img src="'>>$output_html
			basename ${input.file_name} >>$output_html
			echo '.quality.jpg"&#62;'>>$output_html
			echo '&#60;p&#62;&#60;a href="'>>$output_html
			basename ${input.file_name} >>$output_html
			echo '.quality.pdf"&#62;Download quality in PDF format&#60;/a&#62;&#60;/p&#62;'>>$output_html
				
			echo "&#60;p&#62;&#60;h2&#62;Distribution of longest read segments passing the threshold:&#60;/h2&#62;&#60;/p&#62;">>$output_html
			echo '&#60;img src="'>>$output_html
			basename ${input.file_name} >>$output_html
			echo '.segments.hist.jpg"&#62;'>>$output_html
			echo '&#60;p&#62;&#60;a href="'>>$output_html
			basename ${input.file_name} >>$output_html
			echo '.segments.hist.pdf"&#62;Download segments in PDF format&#60;/a&#62;&#60;/p&#62;'>>$output_html	
		#end if
		
		## Coverage estimation
		#if $CovE.value == True and ($input.ext == "sam" or $input.ext == "bam")
		        echo '&#60;hr/&#62;&#60;h2&#62;Coverage Estimation &#60;/h2&#62;'>>$output_html
                        if test \$cov_file_available = 'False'
                        then
                                echo "&#60;p&#62;Warning: Due to coverage processing issues, the job could not be run. Please contact the person in charge or try to re-run the tool.&#60;/p&#62;">>$output_html
                        else
                                wig_file_name=/tmp/\$(basename ${input.file_name})_${window}.wig
                                python ${ os.getcwd() }/${ $__app__.config.tool_path }/EMBL_tools/cov_to_wig.py \$cov_file_name \$wig_file_name `basename ${input.file_name}` ${input.metadata.dbkey} ${window} >>$output_html
                                ln -s \$wig_file_name ${output_html.extra_files_path}/\$(basename \$wig_file_name)
                                checkStatus "Cov to wig conversion failed."
                                echo '&#60;p&#62;&#60;a href="'>>$output_html
                                echo \$(basename \$wig_file_name) >>$output_html
                                echo '"&#62;Download the coverage in WIG format&#60;/a&#62;&#60;/p&#62;'>>$output_html
                        fi
		#end if
		
		## Data on target
		#if $DoT.value == True and ($input.ext == "sam" or $input.ext == "bam")
                        echo '&#60;hr/&#62;&#60;h2&#62;Data on Target &#60;/h2&#62;'>>$output_html
                        if test \$cov_file_available = 'False'
                        then
                                echo "&#60;p&#62;Warning: Due to coverage processing issues, the job could not be run. Please contact the person in charge or try to re-run the tool.&#60;/p&#62;">>$output_html
                        else
                                python ${ os.getcwd() }/${ $__app__.config.tool_path }/EMBL_tools/data_on_target.py \$cov_file_name ${DoT_chr} ${DoT_start} ${DoT_end} ${window} >>$output_html
                                checkStatus "Data on target analysis failed."
                        fi
		#end if
		
		## G-C coverage
		#if $GC.value == True and ($input.ext == "sam" or $input.ext == "bam")
                        echo '&#60;hr/&#62;&#60;h2&#62;G-C coverage &#60;/h2&#62;'>>$output_html
                        if test \$cov_file_available = 'False'
                        then
                                echo "&#60;p&#62;Warning: Due to coverage processing issues, the job could not be run. Please contact the person in charge or try to re-run the tool.&#60;/p&#62;">>$output_html
                        else
                                if test \$gc_file_available = 'False'
                                then
                                        echo "&#60;p&#62;Warning: Due to GC content processing issues, the job could not be run. Please contact the person in charge or try to re-run the tool.&#60;/p&#62;">>$output_html
                                else
                                        R --vanilla --args \$cov_file_name \$gc_file_name ${output_html.extra_files_path}/gcplot.pdf &#60; ${ os.getcwd() }/${ $__app__.config.tool_path }/EMBL_tools/gcPlot.R 2>&#38;1 /dev/null
                                        checkStatus "GC plotting failed."
                                        convert ${output_html.extra_files_path}/gcplot.pdf ${output_html.extra_files_path}/gcplot.jpg
			                checkStatus "GC PDF output convert processing failed."
                                        echo '&#60;img src="gcplot.jpg"&#62;'>>$output_html
                                        echo '&#60;p&#62;&#60;a href="gcplot.pdf"&#62;Download GC coverage in PDF format&#60;/a&#62;&#60;/p&#62;'>>$output_html
                                fi
                        fi
		#end if
		
		## scatterplot process 
		#if $scatterplot.value == True and $input.ext == "bam"
		        echo '&#60;hr/&#62;&#60;h2&#62;+/- strand scatterplot&#60;/h2&#62;'>>$output_html
			/g/steinmetz/collaboration/software/CentOS5/bin/R --vanilla --args ${input.file_name} ${output_html.extra_files_path}/pmscatterplot.png $bin_size &#60;${ os.getcwd() }/${ $__app__.config.tool_path }/EMBL_tools/plus_minus_scatterplot.R 2>&#38;1 /g/funcgen/galaxy/erreurs.txt
			checkStatus "+/- strand scatterplot generation failed."
			echo '&#60;img src="pmscatterplot.png"&#62;'>>$output_html
		#end if
		
		echo '&#60;/body&#62;&#60;/html&#62;' >> $output_html
	  </configfile>
	</configfiles>
	<outputs>
		<data format="html" name="output_html"/>
	</outputs>
<help>
.. class:: warningmark

Please read!

If you wish to run all the programs available for your input file type, just leave all the checkboxes checked, if a program can't run on it, it will be **automatically inactivated**.

The results are gathered in a single HTML output file that can be read by **clicking on the eye** of the result in your history.

_______________________________________________________________________________________________

.. class:: infomark

Here is what will run according to the file type:

_______________________________________________________________________________________________

+-----------------+-------+--------+-----+-----+
|                 | FASTQ | Export | SAM | BAM |
+-----------------+-------+--------+-----+-----+
| R QA            |       |    +   |     |     |
+-----------------+-------+--------+-----+-----+
| HTSeq           |   +   |        |  +  |  +  |
+-----------------+-------+--------+-----+-----+
| baseQual        |   +   |        |     |     |
+-----------------+-------+--------+-----+-----+
| SolexaQA        |   +   |        |     |     |
+-----------------+-------+--------+-----+-----+
| Coverage        |       |        |  +  |  +  |
+-----------------+-------+--------+-----+-----+
| Data on target  |       |        |  +  |  +  |
+-----------------+-------+--------+-----+-----+
| GC content      |       |        |  +  |  +  |
+-----------------+-------+--------+-----+-----+
| Mappability     |       |        |     |     |
+-----------------+-------+--------+-----+-----+
| Redundancy/Uniq |       |        |     |     |
+-----------------+-------+--------+-----+-----+
| Yield           |       |        |     |     |
+-----------------+-------+--------+-----+-----+
| +/- scatterplot |       |        |     |  +  |
+-----------------+-------+--------+-----+-----+

_______________________________________________________________________________________________

.. class:: infomark

Here is the detail of each program:

_______________________________________________________________________________________________

---- **R QA** ----

Does QA of export files and save it at given directory. The output is a report in html format.

---- **HTSeq-qa** ----

This script takes a file with high-throughput sequencing reads (supported
formats: SAM, Solexa _export.txt, FASTQ, Solexa _sequence.txt) and performs a
simple quality assessment by producing plots showing the distribution of
called bases and base-call quality scores by position within the reads. The
plots are gathered in a single PDF file.

Options:
  **type**  type of read_file (one of: sam , solexa-export, fastq, solexa-fastq [default])

HTSeq-qa is part of  'HTSeq' framework, you can use it out of galaxy.

Written by Simon Anders (sand...@fs.tum.de), European Molecular Biology
Laboratory (EMBL). (c) 2010. Released under the terms of the GNU General
Public License v3. Part of the 'HTSeq' framework, version 0.4.4.

---- **baseQual** ----

Works with fastq files, outputs a table with the average quality score for each base position of the reads.

---- **SolexaQA** ----

This software produces a heatmap of the quality by base position and by tile, a plot of the distribution of the mean quality, and a histogram of the distribution of the longest read segments passing the quality threshold.
For more information, please see the related article: http://www.biomedcentral.com/1471-2105/11/485

---- **Coverage** ----

The main software for the coverage analysis was written by Tobias Rausch (rau...@embl.de) (c) Copyright 2009 (EMBL: GeneCore, Korbel group):

**Cov:** Calculates the average or base-pair coverage for non-overlapping, overlapping or custom defined intervals.

This wrapper produces a WIG file containing the coverage estimation calculated by **cov**. The window size for the esstimation can be set according to the contents of the input dataset.

---- **Data on target** ----

This program uses the same software as for the coverage estimation (see *Coverage*).

This tool compares the coverage inside and outside the target. It can manage only one target, and the windows containing the start or the end of the target are omitted. As a result, the target **must** be at least twice as big as the windows. Please make sure you pick an appropriate window size.

The percentage of reads, the mean coverage and the median coverage are calculated inside and outside the target and the results are displayed in a table.

---- **GC content** ----

This script generates a plot of the coverage vs the GC content of the windows generated by cov (*see Coverage*). It was written by Thomas Zichner (zich...@embl.de).

---- **Mappability** ----

*Not implemented yet.*

---- **Redundancy/Uniqueness** ----

*Not implemented yet.*

---- **Yield** ----

*Not implemented yet.*

---- **+/- strand scatterplot** ----

This program is a R script that uses the *Rsamtools* and *HistoneChIPseq* packages. It was written by Nicolas Delhomme (delho...@embl.de) and Louise-Amélie Schmitt (schm...@embl.de). It produces two plots from the same data, one with the actual data represented by dots and a smooth scatterplot to highlight the highly populated zones. The axes are logarithmic.

You can set the window(bin) size with the selector, to tune the results according to the contents of the input data.

</help>
</tool>	
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