Mercurial > repos > galaxyp > idconvert
diff idconvert.xml @ 2:edb33e8224c6 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
| author | galaxyp |
|---|---|
| date | Sat, 23 Feb 2019 06:21:11 -0500 |
| parents | 9e6e840d6b52 |
| children |
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--- a/idconvert.xml Mon Aug 08 10:43:52 2016 -0400 +++ b/idconvert.xml Sat Feb 23 06:21:11 2019 -0500 @@ -1,9 +1,8 @@ <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" /> + <requirements> + <requirement type="package" version="3.0.9992">proteowizard</requirement> + </requirements> <stdio> <exit_code range="1:" /> <regex match="Error" @@ -15,15 +14,15 @@ <![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 $input_name +ln -s '$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/* $output +--outdir 'outdir' +&& cp outdir/* '$output' ]]> </command> <inputs> @@ -49,40 +48,40 @@ <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> + </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. @@ -118,6 +117,8 @@ idconvert mascot.mzid --pepXML ]]> - </help> - <expand macro="citations" /> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btn323</citation> + </citations> </tool>