Mercurial > repos > galaxyp > msgfplus
changeset 6:4b7d768b74d3 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 11837caf01413f2657b529b7cd7a4ec0960110fa
| author | galaxyp |
|---|---|
| date | Fri, 27 Oct 2017 13:04:49 -0400 |
| parents | ce4882b95b73 |
| children | f8873f2afc6f |
| files | msgfplus.xml |
| diffstat | 1 files changed, 32 insertions(+), 24 deletions(-) [+] |
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--- a/msgfplus.xml Wed Sep 13 15:57:41 2017 -0400 +++ b/msgfplus.xml Fri Oct 27 13:04:49 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="msgfplus" name="MS-GF+" version="0.3"> +<tool id="msgfplus" name="MS-GF+" version="0.3.1"> <description> Identifies peptides in tandem mass spectra using the MS-GF+ search engine. </description> @@ -33,10 +33,11 @@ #end for #for $mod in $custom_mods - echo '${mod.formula_or_mass},${mod.aa_specificity},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt && + #set aa_nocomma = str($mod.aa_specificity).replace(",", "") + echo '${mod.formula_or_mass},${aa_nocomma},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt && #end for - msgf_plus + msgf_plus -s '$input_name' -d '$db_name' -thread \${GALAXY_SLOTS:-1} @@ -55,31 +56,31 @@ -maxCharge $advanced.maxCharge -n $advanced.n -addFeatures $advanced.addFeatures - #if $tsvcheck - && - msgf_plus - edu.ucsd.msjava.ui.MzIDToTsv - -i '$output_name' - -o output.tsv - #end if + #if $tsvcheck + && + msgf_plus + edu.ucsd.msjava.ui.MzIDToTsv + -i '$output_name' + -o output.tsv + #end if && mv '$output_name' output ]]> </command> <inputs> <conditional name="msgf_input"> - <param name="intype_selector" type="select" label="Type of MSGF+ analysis"> - <option value="single">Single database</option> - <option value="fractions">Prefractionated database</option> - </param> - <when value="single"> - <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/> - <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/> - </when> - <when value="fractions"> - <param name="db_spectra" type="data_collection" collection_type="paired" - label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/> - </when> + <param name="intype_selector" type="select" label="Type of MSGF+ analysis"> + <option value="single">Single database</option> + <option value="fractions">Prefractionated database</option> + </param> + <when value="single"> + <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/> + <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/> + </when> + <when value="fractions"> + <param name="db_spectra" type="data_collection" collection_type="paired" + label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/> + </when> </conditional> <param name="tsvcheck" type="boolean" label="Output TSV as well?" /> <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" /> @@ -305,8 +306,15 @@ <param name="custom_mods_1|fix_or_opt" value="opt" /> <param name="custom_mods_1|position_specificity" value="any" /> <param name="custom_mods_1|mod_name" value="cGMP" /> - - <output name="output" file="201208-378803-msgf_20161026-2mmu-tryptic-many_mods.mzid" lines_diff="6" /> + + <output name="output"> + <assert_contents> + <has_text text="iTRAQ4plex" /> + <has_text text="pyro-Glu" /> + <has_text text="Gly-loss" /> + <has_text text="cGMP" /> + </assert_contents> + </output> </test> </tests> <help>