Mercurial > repos > galaxyp > percolator
diff msgf2pin.xml @ 1:86770eea5b09 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
author | galaxyp |
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date | Sat, 04 Mar 2017 20:36:03 -0500 |
parents | 3a49065a05d6 |
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--- a/msgf2pin.xml Wed Dec 07 16:43:51 2016 -0500 +++ b/msgf2pin.xml Sat Mar 04 20:36:03 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="msgfplus2pin" name="MS-GF+ output to Pin converter" version="3.0"> +<tool id="msgfplus2pin" name="MS-GF+ output to Pin converter" version="3.0.1"> <description>to create Percolator input files</description> <requirements> <requirement type="package" version="3.0">percolator</requirement> @@ -6,17 +6,50 @@ <stdio> <exit_code range="1:"/> </stdio> - <command> - msgf2pin -o $pinout -e $enzyme - #if $matches - -m $matches + <command><![CDATA[ + mkdir target && mkdir decoy && + + #if $mzids.inputtype == "multi" + #for $key in $mzids.target.keys() + ln -s '$mzids.target[$key]' 'target/$key' && + echo 'target/$key' >> targetmeta && + #end for + #for $key in $mzids.decoy.keys() + ln -s '$mzids.decoy[$key]' 'decoy/$key' && + echo 'decoy/$key' >> decoymeta && + #end for + msgf2pin -o $pinout -e $enzyme + #if $matches + -m $matches + #end if + $aafreq $ptm $pngase $isotope targetmeta decoymeta + + #else + ln -s '$mzids.target' 'target/$target.display_name' && + ln -s '$mzids.decoy' 'decoy/$decoy.display_name' && + msgf2pin -o $pinout -e $enzyme + #if $matches + -m $matches + #end if + $aafreq $ptm $pngase $isotope + 'target/$mzids.target.display_name' 'decoy/$mzids.decoy.display_name' #end if - $aafreq $ptm $pngase $isotope - "$target" "$decoy" - </command> + ]]></command> <inputs> - <param name="target" type="data" format="mzid,meta2pin" label="Target MSGF+ results or metafile pointing to them" /> - <param name="decoy" type="data" format="mzid,meta2pin" label="Decoy MSGF+ results or metafile pointing to them" /> + <conditional name="mzids"> + <param name="inputtype" type="select" display="radio"> + <option value="single">Single mzIdentML</option> + <option value="multi">Multiple mzIdentMLs</option> + </param> + <when value="single"> + <param name="target" type="data" format="mzid" label="Target MSGF+ results" /> + <param name="decoy" type="data" format="mzid" label="Decoy MSGF+ results" /> + </when> + <when value="multi"> + <param name="target" type="data_collection" collection_type="list" format="mzid" label="Target MSGF+ results" /> + <param name="decoy" type="data_collection" collection_type="list" format="mzid" label="Decoy MSGF+ results" /> + </when> + </conditional> <param name="enzyme" type="select" label="Enzyme used"> <option value="trypsin">trypsin</option> <option value="no_enzyme">no enzyme</option> @@ -42,22 +75,40 @@ </outputs> <tests> <test> - <param name="target" value="target.mzid"/> - <param name="decoy" value="decoy.mzid"/> + <param name="mzids|inputtype" value="single" /> + <param name="mzids|target" value="target.mzid" /> + <param name="mzids|decoy" value="decoy.mzid" /> <param name="ptm" value="true"/> <param name="matches" value="1"/> <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" /> </test> + <test> + <param name="mzids|inputtype" value="multi" /> + <param name="mzids|target"> + <collection type="list"> + <element name="target1" value="target.mzid" /> + <element name="target2" value="target.mzid" /> + </collection> + </param> + <param name="mzids|decoy"> + <collection type="list"> + <element name="decoy1" value="decoy.mzid" /> + <element name="decoy2" value="decoy.mzid" /> + </collection> + </param> + <param name="ptm" value="true"/> + <param name="matches" value="1"/> + <output name="pinout" value="percolatorInresult_multifractions.txt" compare="sim_size" delta="20" /> + </test> </tests> <help> The percolator converter msgf2pin converts mzIdentML to input for percolator. Target and decoy inputs are MzIdentML-files of MS-GF+ from separate target and decoy searches. Internal MS-GF+ target/decoy analysis should be turned off, and the addFeatures options turned on. -Multiple MzIdentML-files can be merged by replacing target and decoy -filepaths with meta files. Meta files are text files containing the -the paths of mzid-files, one path per line. For successful results, -the different runs should be generated under similar conditions. +Multiple MzIdentML-files can be merged by passing lists of these. +For successful results, the different runs should be generated under +similar conditions. </help> <citations> <citation type="doi">10.1021/pr400937n</citation>