comparison idconvert.xml @ 2:edb33e8224c6 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292

1:9e6e840d6b52

<tool id="idconvert" name="idconvert" version="@VERSION@.0">
    <description>Convert mass spectrometry identification files</description>
    <macros>
        <import>msconvert_macros.xml</import>
    </macros>
    <expand macro="generic_requirements" />
    <stdio>
        <exit_code range="1:" />
        <regex match="Error"
           source="both"
           level="fatal"

    </stdio>
    <command>
<![CDATA[
#import os.path
#set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')])
ln -s "$from.input" "$input_name" &&
idconvert $input_name 
#if str($to_format) == 'pep.xml':
--pepXML
#elif str($to_format) == 'text':
--text
#end if
--outdir outdir 
&& cp outdir/* $output
]]>
    </command>
    <inputs> 
        <conditional name="from">
            <param name="from_format" type="select" label="Convert from">

        <param name="to_format" type="select" label="Convert to">
            <option value="mzid">mzIdentML (mzid)</option>
            <option value="pep.xml">pepXML (pepxml)</option>
            <option value="text">text</option>
        </param>
  </inputs>
  <outputs>
      <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}">
        <change_format>
          <when input="to_format" value="pep.xml" format="pepxml" />
          <when input="to_format" value="text" format="txt" />
        </change_format>
      </data>
  </outputs>
  <tests>
      <test>
          <param name="input" value="Rpal_01.pepXML" />
          <param name="from_format" value="pepxml" />
          <param name="to_format" value="mzid" />
          <output name="output_psms">
              <assert_contents>
                  <has_text text="MzIdentML" />
                  <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
              </assert_contents>
          </output>
      </test>
      <test>
          <param name="input" value="Rpal_01.mzid" />
          <param name="from_format" value="mzid" />
          <param name="to_format" value="pep.xml" />
          <output name="output_psms">
              <assert_contents>
                  <has_text text="msms_pipeline_analysis" />
                  <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
              </assert_contents>
          </output>
      </test>
  </tests>
  <help>
<![CDATA[
idconvert [options] [filemasks]
Convert mass spec identification file formats.

Return value: # of failed files.

# convert mascot.mzid to mascot.pepXML
idconvert mascot.mzid --pepXML

]]>
  </help>
  <expand macro="citations" />
</tool>

2:edb33e8224c6

<tool id="idconvert" name="idconvert" version="@VERSION@.0">
    <description>Convert mass spectrometry identification files</description>
    <requirements>
      <requirement type="package" version="3.0.9992">proteowizard</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <regex match="Error"
           source="both"
           level="fatal"

    </stdio>
    <command>
<![CDATA[
#import os.path
#set $input_name = '.'.join([$os.path.basename(str($from.input)),str($from.input.extension).replace('xml','.xml')])
ln -s '$from.input' '$input_name' &&
idconvert '$input_name'
#if str($to_format) == 'pep.xml':
--pepXML
#elif str($to_format) == 'text':
--text
#end if
--outdir 'outdir'
&& cp outdir/* '$output'
]]>
    </command>
    <inputs> 
        <conditional name="from">
            <param name="from_format" type="select" label="Convert from">

        <param name="to_format" type="select" label="Convert to">
            <option value="mzid">mzIdentML (mzid)</option>
            <option value="pep.xml">pepXML (pepxml)</option>
            <option value="text">text</option>
        </param>
    </inputs>
    <outputs>
        <data format="mzid" name="output" label="${from.input.name.rsplit('.',1)[0]}.${to_format}">
            <change_format>
                <when input="to_format" value="pep.xml" format="pepxml" />
                <when input="to_format" value="text" format="txt" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="Rpal_01.pepXML" />
            <param name="from_format" value="pepxml" />
            <param name="to_format" value="mzid" />
            <output name="output">
                <assert_contents>
                    <has_text text="MzIdentML" />
                    <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="Rpal_01.mzid" />
            <param name="from_format" value="mzid" />
            <param name="to_format" value="pep.xml" />
            <output name="output">
                <assert_contents>
                    <has_text text="msms_pipeline_analysis" />
                    <has_text text="VIKKSTTGRVLSDDILVIRKGEIAARNASHKMR" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
idconvert [options] [filemasks]
Convert mass spec identification file formats.

Return value: # of failed files.

# convert mascot.mzid to mascot.pepXML
idconvert mascot.mzid --pepXML

]]>
    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btn323</citation>
    </citations>
</tool>