Re: [galaxy-dev] outputs label attribute

14 Aug 2013

      Hi Bjoern,

       Many thanks for your reply.
Here is the wrapper:
<tool id="proteowizard" name="Convert spectral file into mzML file" version="1.0.0">
    <description>Convert non PSI standard mass spectral file into the PSI standard format mzML</description>
        <command interpreter="perl">$__root_dir__/../gio_applications/proteowizard/proteowizard.pl $input $type.input_type $output $output.id $__new_file_path__</command>
    <inputs>
    	<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>
            </param>
            <when value="mgf">
		<param format="mgf" name="input" type="data" label="Input mgf"/>
            </when>
            <when value="mzxml">
		<param format="mzxml" name="input" type="data" label="Input mzXML"/>
            </when>
            <when value="ms2">
        	<param format="ms2" name="input" type="data" label="Input ms2"/>
            </when>
	</conditional>
    </inputs>
    <outputs>
	<data name="output" format="mzml"/>
    </outputs>
</tool>
and the corresponding perl script:
#!/usr/bin/perl -w
use strict;

my $input = $ARGV[0];
my $type = $ARGV[1];
my $output = $ARGV[2];
my $id = $ARGV[3];
my $path = $ARGV[4];

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
system("/$path/../../../gio_applications/proteowizard/msconvert /$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!
Jun

-----Original Message-----
From: Bjoern Gruening [mailto:bjoern.gruening@gmail.com] 
Sent: 14 August 2013 08:29
To: Jun Fan
Cc: galaxy-dev@lists.bx.psu.edu
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))[0]#-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.

http://wiki.galaxyproject.org/Events/GCC2013/BoF/ToolDevelopers

Cheers,
Bjoern
...
Look forward to your kind answers. Many thanks in advance.
Best regards!
Jun
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