please have a look at
the else clause will create some symlinks you can use directly with
msconvert. For debugging purpose just add msconvert at first to your
PATH and avoid the $__root_dir__/ hack. Later there are better
approaches to do so.
Also pleaes note that msconvert is already in the toolshed:
There is an entire project called galaxyp
(https://bitbucket.org/galaxyp) driven by John Chilton and Ira Cooke.
> Hi Bjoern,
> Many thanks for your reply.
> Here is the wrapper:
> <tool id="proteowizard" name="Convert spectral file into mzML file"
> <description>Convert non PSI standard mass spectral file into the PSI
> standard format mzML</description>
> $input $type.input_type $output $output.id $__new_file_path__</command>
> <conditional name="type">
> <param name="input_type" type="select" label="Input Type">
> <option value="mgf">mgf</option>
> <option value="mzxml">mzXML</option>
> <option value="ms2">ms2</option>
> <when value="mgf">
> <param format="mgf" name="input" type="data" label="Input mgf"/>
> <when value="mzxml">
> <param format="mzxml" name="input" type="data" label="Input
> <when value="ms2">
> <param format="ms2" name="input" type="data" label="Input ms2"/>
> <data name="output" format="mzml"/>
> and the corresponding perl script:
> #!/usr/bin/perl -w
> use strict;
> my $input = $ARGV;
> my $type = $ARGV;
> my $output = $ARGV;
> my $id = $ARGV;
> my $path = $ARGV;
> system("cp $input /$path/tmp_$id.$type"); #copy the input file to the temp
> folder and rename it to a temp file using the job id to be unique
> /$path/tmp_$id.$type --outfile tmp_$id.mzML -o $path"); #do the conversion
> and keeps the result file in the temp folder
> system("mv /$path/tmp_$id.mzML $output"); #move the result file from the temp
> folder to the galaxy
> system("rm /$path/tmp_$id.$type"); #delete the temp file
> Best regards!
> -----Original Message-----
> From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]
> Sent: 14 August 2013 08:29
> To: Jun Fan
> Cc: firstname.lastname@example.org
> Subject: Re: [galaxy-dev] outputs label attribute
> Hi Jun,
> > I have managed to use something like
> > <outputs>
> > <data format="fasta" name="output" label="#echo os.path.splitext
> > (str ($input.name))#-ORF.fasta"/>
> > </outputs> to display the wanted label for the dataset in the
> > history.
> > However when I applied the same code to other tool wrappers, some
> > weird things happened: the wrapper can still be loaded in the web
> > page, but when I click the execute button to submit the job, nothing
> > happened except the web browser giving the status “wait for
> > localhost”.
> > I cannot think of any reason for that. The main difference I can
> > think of between the successful wrapper and the failed ones is that in
> > the failed ones I have to do some file manipulations as galaxy always
> > stores its dataset with the file suffix .dat which is not acceptable
> > in the tool, e.g. proteowizard. I have to rename it with the correct
> > suffix and move the final result to the output file.
> I do not think its related to your label attribute. Can you post you complete
> wrapper? For the file manipulation I usually use symlinks to $TEMP and use
> these symlink as input.
> > Additional related questions:
> > 1. How to display the selected value of a conditional element in
> > the label? $conditional.value?
> Normally you have something like that in your condition, or?
> <conditional name="scaling">
> <param name="type" type="select" label="Scaling/Normalization method" > ....
> You can access the value of param with $scaling.type
> > 2. How to display different strings according to the conditional
> > selection? Similar to command element to use #if #elsif #end if?
> Not tested, but your example above uses cheetah for the splitext function,
> maybe you can try something like that:
> label="#if $scaling.type == 'no': print 'no' #else print 'yes'#"/>
> > 3. When using <data name="output" format="csv">
> > <change_format> <when input="type" value="html" format="html"/>
> > </change_format> </data>, could I use label attribute in the data and
> > when elements?
> No clue, but I don't think that is possible.
> Please keep in mind that the label should be easy to read and to remember,
> I'm not sure your approach to put in every single parameter is ideal. We had
> some discussion about that at the last GCC and we will work on some
> guidelines or better default lables in the future.
> > Look forward to your kind answers. Many thanks in advance.
> > Best regards!
> > Jun
> > ___________________________________________________________
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