Mercurial > repos > galaxyp > morpheus
changeset 3:8295d959ca28 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus commit 84a14a4f77dc68f80e6f7d9ac562b6d9b46d58b1
| author | galaxyp |
|---|---|
| date | Mon, 15 Jul 2024 18:21:24 +0000 |
| parents | e0104a9f20f0 |
| children | |
| files | macros.xml morpheus.xml |
| diffstat | 2 files changed, 129 insertions(+), 47 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jul 15 18:21:24 2024 +0000 @@ -0,0 +1,77 @@ +<macros> + <token name="@TOOL_VERSION@">288</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.05</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0121</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_2479</edam_operation> + <edam_operation>operation_3092</edam_operation> + </edam_operations> + </xml> + <xml name="biotools"> + <xrefs> + <xref type="bio.tools">morpheus</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">morpheus</requirement> + </requirements> + </xml> + <xml name="modification_options"> + <option value="acetylation of protein N-terminus">acetylation of protein N-terminus</option> + <option value="acetylation of lysine">acetylation of lysine</option> + <option value="phosphorylation of S">phosphorylation of S</option> + <option value="phosphorylation of T">phosphorylation of T</option> + <option value="phosphorylation of Y">phosphorylation of Y</option> + <option value="deamidation of N">deamidation of N</option> + <option value="deamidation of Q">deamidation of Q</option> + <option value="pyro-cmC">pyro-cmC</option> + <option value="pyro-E">pyro-E</option> + <option value="pyro-Q">pyro-Q</option> + <option value="TMT zero on peptide N-terminus">TMT zero on peptide N-terminus</option> + <option value="TMT zero on K">TMT zero on K</option> + <option value="TMT zero on Y">TMT zero on Y</option> + <option value="TMT duplex on peptide N-terminus">TMT duplex on peptide N-terminus</option> + <option value="TMT duplex on K">TMT duplex on K</option> + <option value="TMT duplex on Y">TMT duplex on Y</option> + <option value="TMT sixplex/tenplex on peptide N-terminus">TMT sixplex/tenplex on peptide N-terminus</option> + <option value="TMT sixplex/tenplex on K">TMT sixplex/tenplex on K</option> + <option value="TMT sixplex/tenplex on Y">TMT sixplex/tenplex on Y</option> + <option value="iTRAQ 4-plex on peptide N-terminus">iTRAQ 4-plex on peptide N-terminus</option> + <option value="iTRAQ 4-plex on K">iTRAQ 4-plex on K</option> + <option value="iTRAQ 4-plex on Y">iTRAQ 4-plex on Y</option> + <option value="iTRAQ 8-plex on peptide N-terminus">iTRAQ 8-plex on peptide N-terminus</option> + <option value="iTRAQ 8-plex on K">iTRAQ 8-plex on K</option> + <option value="iTRAQ 8-plex on Y ">iTRAQ 8-plex on Y </option> + </xml> + <xml name="variable_modification_options"> + <option value="oxidation of M" selected="true">oxidation of M</option> + <option value="carbamidomethylation of C">carbamidomethylation of C</option> + <expand macro="modification_options"/> + </xml> + <xml name="fixed_modification_options"> + <option value="carbamidomethylation of C" selected="true">carbamidomethylation of C</option> + <option value="oxidation of M">oxidation of M</option> + <expand macro="modification_options"/> + </xml> + <xml name="proteases_options"> + <option value="Arg-C">Arg-C</option> + <option value="Asp-N" >Asp-N</option> + <option value="chymotrypsin (no proline rule)" >chymotrypsin (no proline rule)</option> + <option value="Glu-C" >Glu-C</option> + <option value="Lys-C" >Lys-C</option> + <option value="Lys-C (no proline rule)" >Lys-C (no proline rule)</option> + <option value="Lys-N" >Lys-N</option> + <option value="semi-trypsin" >semi-trypsin</option> + <option value="semi-trypsin (no proline rule)" >semi-trypsin (no proline rule)</option> + <option value="trypsin" >trypsin</option> + <option value="trypsin (no proline rule)" selected="true">trypsin (no proline rule)</option> + <option value="tryptophan oxidation" >tryptophan oxidation</option> + <option value="non-specific" >non-specific</option> + <option value="top-down" >top-down</option> + </xml> +</macros>
--- a/morpheus.xml Thu Jan 12 15:50:48 2017 -0500 +++ b/morpheus.xml Mon Jul 15 18:21:24 2024 +0000 @@ -1,49 +1,11 @@ -<tool id="morpheus" name="Morpheus" version="2.255.0"> +<tool id="morpheus" name="Morpheus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>database search algorithm for high-resolution tandem mass spectra</description> <macros> - <xml name="modification_options"> - <option value="acetylation of protein N-terminus">acetylation of protein N-terminus</option> - <option value="acetylation of lysine">acetylation of lysine</option> - <option value="phosphorylation of S">phosphorylation of S</option> - <option value="phosphorylation of T">phosphorylation of T</option> - <option value="phosphorylation of Y">phosphorylation of Y</option> - <option value="deamidation of N">deamidation of N</option> - <option value="deamidation of Q">deamidation of Q</option> - <option value="pyro-cmC">pyro-cmC</option> - <option value="pyro-E">pyro-E</option> - <option value="pyro-Q">pyro-Q</option> - <option value="TMT zero on peptide N-terminus">TMT zero on peptide N-terminus</option> - <option value="TMT zero on K">TMT zero on K</option> - <option value="TMT zero on Y">TMT zero on Y</option> - <option value="TMT duplex on peptide N-terminus">TMT duplex on peptide N-terminus</option> - <option value="TMT duplex on K">TMT duplex on K</option> - <option value="TMT duplex on Y">TMT duplex on Y</option> - <option value="TMT sixplex/tenplex on peptide N-terminus">TMT sixplex/tenplex on peptide N-terminus</option> - <option value="TMT sixplex/tenplex on K">TMT sixplex/tenplex on K</option> - <option value="TMT sixplex/tenplex on Y">TMT sixplex/tenplex on Y</option> - <option value="iTRAQ 4-plex on peptide N-terminus">iTRAQ 4-plex on peptide N-terminus</option> - <option value="iTRAQ 4-plex on K">iTRAQ 4-plex on K</option> - <option value="iTRAQ 4-plex on Y">iTRAQ 4-plex on Y</option> - <option value="iTRAQ 8-plex on peptide N-terminus">iTRAQ 8-plex on peptide N-terminus</option> - <option value="iTRAQ 8-plex on K">iTRAQ 8-plex on K</option> - <option value="iTRAQ 8-plex on Y ">iTRAQ 8-plex on Y </option> - </xml> - <xml name="variable_modification_options"> - <option value="oxidation of M" selected="true">oxidation of M</option> - <option value="carbamidomethylation of C">carbamidomethylation of C</option> - <expand macro="modification_options"/> - </xml> - <xml name="fixed_modification_options"> - <option value="carbamidomethylation of C" selected="true">carbamidomethylation of C</option> - <option value="oxidation of M">oxidation of M</option> - <expand macro="modification_options"/> - </xml> + <import>macros.xml</import> </macros> - - <requirements> - <requirement type="package" version="255">morpheus</requirement> - </requirements> - + <expand macro="edam_ontology"/> + <expand macro="biotools"/> + <expand macro="requirements"/> <stdio> <exit_code range="1:" /> <regex match="System..*Exception" @@ -150,7 +112,10 @@ #if str($vm) != 'None': #set $vmods = str($vm).replace(',',';') -vm="$vmods" - #end if + #end if + #if str($p) != 'None': + -p="$p" + #end if -mt=\${GALAXY_SLOTS:-4} #set $out_list = 'log.txt summary.tsv aggregate.PSMs.tsv aggregate.unique_peptides.tsv aggregate.protein_groups.tsv aggregate.mzid *.pep.xml' #if len($input_list) == 1: @@ -171,7 +136,10 @@ </param> <param name="vm" type="select" multiple="true" optional="true" label="Variable Modifications"> <expand macro="variable_modification_options" /> - </param> + </param> + <param name="p" type="select" label="Proteases"> + <expand macro="proteases_options"/> + </param> <param name="fdr" type="float" value="1" optional="true" min="0.0" max="100.0" label="FDR (Maximum False Discovery Rate percent)" /> <param name="mvmi" type="integer" value="1024" optional="true" min="0" label="Maximum Variable Modification Isoforms Per Peptide" /> <param name="precmtv" type="float" value="10." optional="true" label="Precursor Mass Tolerance Value" /> @@ -270,6 +238,24 @@ <not_has_text text="K.TTGSSSSSSSK.K" /> </assert_contents> </output> + </test> + <test> + <param name="inputs" value="test_input.mzML" ftype="mzml"/> + <param name="searchdb" value="uniprot-proteome_UP000002311-first100entries.fasta" ftype="fasta"/> + <param name="fdr" value="1"/> + <param name="mvmi" value="1024"/> + <param name="precmt" value="Monoisotopic"/> + <param name="precmtu" value="Da"/> + <param name="precmtv" value="2.5"/> + <param name="fm" value="carbamidomethylation of C"/> + <param name="vm" value="oxidation of M"/> + <param name="p" value="trypsin" /> + <output name="output_psms"> + <assert_contents> + <has_text text="K.DGM(oxidation of M)KAYAQNVQQR.E" /> + <not_has_text text="K.TTGSSSSSSSK.K" /> + </assert_contents> + </output> </test> <test> <param name="inputs" value="test_input.mzML" ftype="mzml"/> @@ -283,7 +269,7 @@ <param name="vm" value="oxidation of M"/> <output name="output_psms"> <assert_contents> - <has_text text="R.KRSLFDS(UniProt: Phosphoserine)AFSSR.A" /> + <has_text text="K.RSPSGNISTNSMR.P" /> <not_has_text text="K.KYFLENKIGTDR.R" /> </assert_contents> </output> @@ -307,7 +293,26 @@ </assert_contents> </output> </test> - + <test> + <param name="inputs" value="test_input.mzML" ftype="mzml"/> + <param name="searchdb" value="uniprot-proteome_UP000002311Condensed-first100entries.xml" ftype="uniprotxml"/> + <param name="fdr" value="1"/> + <param name="mvmi" value="1024"/> + <param name="precmt" value="Monoisotopic"/> + <param name="precmtu" value="Da"/> + <param name="precmtv" value="2.5"/> + <param name="fm" value="carbamidomethylation of C"/> + <param name="vm" value="oxidation of M"/> + <param name="p" value="trypsin"/> + <param name="adv_options_selector" value="set"/> + <param name="prodmtv" value=".01"/> + <output name="output_psms"> + <assert_contents> + <has_text text="K.KTLKSDGVAGLYR.G" /> + <not_has_text text="K.KYFLENKIGTDR.R" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ Morpheus_ is a database search algorithm for high-resolution tandem mass spectra.