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Merge pull request #766 from mthang/morpheus_enzyme_option
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add enzyme list to morpheus tool
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@bgruening
bgruening authored Jul 15, 2024
2 parents 408c202 + dd82962 commit 84a14a4
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Showing 3 changed files with 130 additions and 47 deletions.
1 change: 1 addition & 0 deletions tools/morpheus/.shed.yml
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Expand Up @@ -3,6 +3,7 @@ name: morpheus
categories:
- Proteomics
description: Morpheus MS Search Application
homepage_url: https://cwenger.github.io/Morpheus
long_description: |
Morpheus database search algorithm for high-resolution tandem mass spectra.
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77 changes: 77 additions & 0 deletions tools/morpheus/macros.xml
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<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>
99 changes: 52 additions & 47 deletions tools/morpheus/morpheus.xml
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@@ -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"
Expand Down Expand Up @@ -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:
Expand All @@ -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" />
Expand Down Expand Up @@ -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"/>
Expand All @@ -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>
Expand All @@ -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.
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