Jeremy,

Thanks. The horizontal rule is working for me now.
An example of the second item is attached in XML file. The last list at the
bottom doesn't render a blank line after the last list item, but used to.

Rgds,
Greg


On Tue, Mar 27, 2012 at 11:51 PM, Jeremy Goecks <jeremy.goe...@emory.edu>wrote:

> Greg,
>
> 1. The horizontal rule dividers specified by a "-----" in the text have
> disappeared.
>
>
> Fixed in galaxy-central changeset cb5ff5b1bd67
>
> 2. Also I spotted a change where this ..
>
> *- line 1 of some bullets*
> *- line 2 of some bullets*
> *
> *
> *Following line*.
>
> .. lost the blank line after the "line 2" line.
>
>
> Where exactly is this occurring?
>
> Thanks for the feedback,
> J.
>
>


-- 
Greg Edwards,
Port Jackson Bioinformatics
gedwar...@gmail.com
<!-- 

  VERSION: 26mar12
  Also update version at bottom
  
-->

<tool id="ptm_tools_1" name="Report phospho sites" version="1.0.0">

  <description>in a peptide set</description>

  <command interpreter="perl">reportSites.pl 
    -galaxy 1
    -galaxydebug 0
    -pep       val=$pepfile 
    -columns   val=$columns 
    -db        val=$dbfile
    -dbtype    val=$dbtype
    -progressemailid    val=$progressemailid
    -progressemailmins  val=$progressemailmins
    -pidprefix val=$pidprefix 
    -htmlout   val=$htmlout
    -guihelp   $guihelp
    -rundescription "$rundescription"
    $extra_args
                
    -galaxy__new_file_path__    $__new_file_path__ 
    -galaxy__tool_data_path__   $__tool_data_path__  
    -galaxy__root_dir__         $__root_dir__        
    -galaxy__datatypes_config__ $__datatypes_config__
    -galaxy__user_id__          $__user_id__         
    -galaxy__user_email__       $__user_email__      
    -galaxy__app__              $__app__ 
    
  </command>

  <version_command></version_command>
<!--
  <version_command> perl reportSites.pl -version </version_command>
-->

  <inputs>

    <param 
      name="pepfile" 
      type="data" 
      format="csv" 
      label="Peptide data file" 
      size="80"
      help="Peptide csv file, mandatory." 
      optional="false"/>
    
    <param 
      name="columns" 
      type="text" 
      label="Peptide data columns" 
      size="20" 
      value="entry-required"
      help="Columns from peptide csv file: peptide, protein id, description, score1, [ score2, score3, score4 ].
            Numeric or alpha. These are from the peptide data spreadsheet, column A = column 0.
            Only peptide column is mandatory, the tool can report on peptide-only data." 
     optional="false"/>
      
    <param 
      name="dbfile" 
      type="data"
      format="fasta" 
      label="Protein database file" 
      size="80"
      help="Protein database file, optional. 
            Eg. ipi.RAT.v3.52.fasta, NCBI_Vitis_Fasta.fasta, uniprot_sprot.fasta, uniprot_trembl.fasta.
            If omitted, only brief checking and counting of raw sites in the peptide file will be done.
            For advice on uploading large files, eg. > 100Mb that might take more than a few minutes,
            see Uploading Large Data Files on the Info Page." 
      optional="true"/>

      
    <param name="dbtype" type="select" label="Protein database type"
      help="If unsure, view the data set in the History and check the header style. 
      The code can automatically detect the type, to a 99.9% level.">
      <option value="Auto">Automatically Detect</option>
      <option value="IPI">IPI . . . . . . . . . . . . . . Style >IPI:IPI00187591.3|...</option>
      <option value="NCBI">NCBI . . . . . . . . . . . . Style >gi|359493355|...</option>
      <option value="UniProtSwiss">UniProt SwissProt . . Style >sp|Q6GZX4|... </option>
      <option value="UniProtTrembl">UniProt Trembl . . . . Style >tr|A0A171|...</option>
    </param>

    <param 
      name="pidprefix" 
      type="text" 
      label="Prefix for protein ids" 
      size="10" 
      help="Optional. A prefix to add to the database ids to make them match the peptide file ids.
            Example: sp, sp_, IPI, IPI:. (The database ids are generally field 2 of the header line, delimited by | )."
      optional="true"/>

    <param 
      name="progressemailid"
      type="text"
      label="Email id for progress reports"
      size="40"
      value=""
      help="Optional. An email id to send progress reports to for long runs. Example: myn...@somewhere.com"
      optional="true"/>
           
    <param 
      name="progressemailmins"
      type="text"
      label="Minutes between email progress reports"
      size="10"
      value="2"
      help="Optional. Minutes between sending email progress reports. Default 2 minutes."
      optional="true"/>
           
    <param 
      name="extra_args" 
      type="text" 
      label="Extra command line args" 
      size="100"
      help="Optional. Any args accepted by the commandline version of the tool, which make sense in a web-served environment. 
            Examples: -maxpep 100, -stopat percentile, -galaxydebug 1"
      optional="true"/>

    <param name="guihelp" type="select" label="Help options"
      help="Help and information options, from the command-line version.">
      <option value="0">None</option>
      <option value="help">Basic help on options</option>
      <option value="longhelp">Longer help on options</option>
      <option value="examples">Examples of usage</option>
      <option value="doco">Brief program documentation</option>
    </param>

    <param 
      name="rundescription" 
      type="text" 
      label="Run Description" 
      size="2x100" 
      area="True"
      help="Describe the run if needed. This will be displayed at the top of the output." 
     optional="true"/>


  </inputs>
  
  <outputs>
    <data format="html" name="htmlout" value="index.html"/>
  </outputs>

<!-- 
  <tests>
    <test>
      <param name="input" value="fa_gc_content_input.fa"/>
      <output name="out_file1" file="fa_gc_content_output.txt"/>
    </test>
  </tests>
-->

<help>
   

If the above file inputs offer no files to choose from, there are no files of
suitable type in the data file list (ie. History, see right). Upload data files
(protein database, and peptide csv) from your local machine with Get Data / Upload File
from the Tools list. File type can be sensed by the upload, or set in the
upload form, or changed later in the History with the ? or Pencil icon.

To view your results, click on the eye . To download results, click on the floppy disk. 
In the downloaded zip file, open Report_phospho_sites_on_data_nn_and_data_nn.html.


-----

**What it does**

This tool runs the reportSites Perl program, reporting on phosphorylation sites in a peptide set. 

A paper is in publication on the code. Please cite the following if needed:

"ReportSites - a computational method to extract positional and physico-chemical
information from large-scale proteomic post-translational modification datasets",
Journal of Proteomics and Bioinformatics (accepted).  

- Alistair V.G. Edwards
- Gregory J. Edwards
- Martin R. Larsen
- Stuart J. Cordwell

Also see the information under menu item Help / How To Cite Galaxy.

Interface version: 26mar12 (ie. the above input and control form).

</help>
</tool>
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