Mercurial > repos > galaxyp > myrimatch
diff myrimatch.xml @ 3:c5e2f015165d draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 23c80475d116664d179cd42a969b0b6bc33419ad
| author | galaxyp |
|---|---|
| date | Mon, 12 Dec 2016 14:51:10 -0500 |
| parents | 4bb0872e2b5f |
| children | e0584c24d0e7 |
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--- a/myrimatch.xml Thu Jun 02 18:32:04 2016 -0400 +++ b/myrimatch.xml Mon Dec 12 14:51:10 2016 -0500 @@ -1,7 +1,7 @@ <tool id="myrimatch" version="0.1.0" name="MyriMatch"> <description>Identify peptides in tandem mass spectra.</description> <requirements> - <requirement type="package" version="3.0.8789">bumbershoot</requirement> + <requirement type="package" version="3.0.10185">bumbershoot</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> @@ -24,19 +24,13 @@ #for $static_mod in $StaticMods #set $static_mods_str = $static_mods_str + " " + str($static_mod.aa) + " " + str($static_mod.mass) #end for - #for $mod in str($common_fixed_modifications).split(",") - #set $static_mods_str = $static_mods_str + " " + $mod.replace("_", " ") - #end for - #set $static_mods_str = $static_mods_str.strip() + #set $static_mods_str = $static_mods_str.lstrip() #set $dynamic_mods_str = "" #for $dynamic_mod in $DynamicMods #set $dynamic_mods_str = $dynamic_mods_str + " " + str($dynamic_mod.motif) + " * " + str($dynamic_mod.mass) #end for - #for $mod in str($common_variable_modifications).split(",") - #set $dynamic_mods_str = $dynamic_mods_str + " " + $mod.replace("_", " ") - #end for - #set $dynamic_mods_str = $dynamic_mods_str.strip() + #set $dynamic_mods_str = $dynamic_mods_str.lstrip() ln -s '$input' '${input_name}' && ln -s '$ProteinDatabase' '${db_name}' && @@ -77,7 +71,7 @@ ]]> </command> <inputs> - <param name="input" type="data" format="mzml,mzxml,mgf,ms2,h5" label="Input Raw MS File(s)"/> + <param name="input" type="data" format="mzml,mzxml,mgf,ms2,mz5" label="Input Raw MS File(s)"/> <param argument="-OutputFormat" type="select" label="Output Type" help="The file format to use for results of the search."> <option value="pepXML">pepXML</option> <option value="mzid">mzIdentML</option> @@ -89,7 +83,6 @@ <option value="Trypsin">Trypsin (normal trypsin cut, disallows cutting when the site is before a proline)</option> <option value="Chymotrypsin">Chymotrypsin (allows cut after F,Y,W,L. Disallows cutting before proline)</option> <option value="TrypChymo">TrypChymo (combines "Trypsin/P" and "Chymotrypsin" cleavage rules)</option> - <option value="glutamyl endopeptidase">Glu-C</option> <option value="Lys-C">Lys-C</option> <option value="Lys-C/P">Lys-C/P (Lys-C, disallowing cutting before proline)</option> <option value="Asp-N">Asp-N</option> @@ -103,41 +96,13 @@ <option value="0">Non-specific (neither terminus is required to match cleavage rules)</option> </param> <param argument="-MaxMissedCleavages" type="integer" min="0" value="2" label="Maximum Missed Cleavages" help="Candidate peptides with more than this number of uncleaved cleavage sites will be skipped." /> - - <param name="common_fixed_modifications" type="select" label="Common Static Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> - <option value="C_57.021464" selected="true">Carbamidomethyl C</option> - <option value="(_144.102063">iTRAQ 4-plex N-term</option> - <option value="K_144.102063">iTRAQ 4-plex K</option> - <option value="(_225.155833">TMT 2-plex N-term</option> - <option value="K_225.155833">TMT 2-plex K</option> - <option value="(_229.162932">TMT 6-or-10-plex N-term</option> - <option value="K_229.162932">TMT 6-or-10-plex K</option> - <sanitizer invalid_char=""><valid initial="string.printable"><add value="("/><add value=")"/><add value=","/><add value="-"/><add value="_"/></valid><mapping initial="none"></mapping></sanitizer> - </param> - <param name="common_variable_modifications" type="select" label="Common Dynamic Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> - <option value="K_*_42.010565">Acetylation K</option> - <option value="(_*_42.010565">Acetylation Protein N-term</option> - <option value="C_*_57.021464">Carbamidomethyl C</option> - <option value="(_*_57.021464">Carbamidomethyl N-term</option> - <option value="N_*_0.984016">Deamidation N</option> - <option value="Q_*_0.984016">Deamidation Q</option> - <option value="K_*_14.015650">Methylation K</option> - <option value="M_*_15.994915" selected="true">Oxidation M</option> - <option value="S_*_97.976896">Phosphorylation S</option> - <option value="T_*_97.976896">Phosphorylation T</option> - <option value="Y_*_97.976896">Phosphorylation Y</option> - <option value="(E_*_-18.010565">Pyro-glu from E</option> - <option value="(Q_*_-17.026549">Pyro-glu from Q</option> - <sanitizer invalid_char=""><valid initial="string.printable"><add value="("/><add value=")"/><add value=","/><add value="_"/><add value="*"/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer> - </param> - - <repeat name="StaticMods" title="Custom Static Modifications" help="Modifications that are always applied to an amino acid. (-StaticMods)"> + <repeat name="StaticMods" title="Static Modifications" help="Modifications that are always applied to an amino acid. (-StaticMods)"> <param name="aa" type="text" label="Amino Acid"> <sanitizer><valid initial="string.ascii_uppercase"><remove value="B"/><remove value="J"/><remove value="O"/><remove value="Z"/></valid></sanitizer> </param> <param name="mass" type="float" label="Mass" value="0" /> </repeat> - <repeat name="DynamicMods" title="Custom Dynamic Modifications" help="Modifications that can either be present or absent on an amino acid. (-DynamicMods)"> + <repeat name="DynamicMods" title="Dynamic Modifications" help="Modifications that can either be present or absent on an amino acid. (-DynamicMods)"> <param name="motif" type="text" label="Amino Acid Motif"> <sanitizer> <valid initial="string.ascii_uppercase"> @@ -152,7 +117,6 @@ </param> <param name="mass" type="float" label="Mass" value="0" /> </repeat> - <param argument="-MaxDynamicMods" type="integer" min="0" value="4" label="Maximum Dynamic Mods" help="Candidate peptides with more than this number of dynamic modifications will be skipped." /> <section name="tolerance_options" title="M/Z Tolerance Options" expanded="True"> <conditional name="precursor_tolerance"> @@ -225,8 +189,6 @@ <param name="input" value="input/201208-378803.mzML" /> <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" /> <param name="DecoyPrefix" value="XXX_" /> - <param name="common_fixed_modifications" value="" /> - <param name="common_variable_modifications" value="" /> <param name="StaticMods_0|aa" value="C" /> <param name="StaticMods_0|mass" value="58.00548" /> <param name="DynamicMods_0|motif" value="M" /> @@ -249,33 +211,8 @@ <test> <param name="input" value="input/201208-378803.mzML" /> <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" /> - <param name="DecoyPrefix" value="XXX_" /> - <param name="StaticMods_0|aa" value="C" /> - <param name="StaticMods_0|mass" value="58.00548" /> - <param name="DynamicMods_0|motif" value="M" /> - <param name="DynamicMods_0|mass" value="15.9949" /> - <param name="DynamicMods_1|motif" value="(Q" /> - <param name="DynamicMods_1|mass" value="-17.026" /> - <param name="common_fixed_modifications" value="" /> - <param name="common_variable_modifications" value="Q_*_0.984016,N_*_0.984016" /> - <param name="PrecursorMzToleranceRule" value="mono" /> - <param name="MonoPrecursorMzTolerance" value="50" /> - <param name="MinTerminiCleavages" value="1" /> - <param name="MaxMissedCleavages" value="2" /> - <param name="MaxDynamicMods" value="2" /> - <param name="NumChargeStates" value="5" /> - <param name="MaxResultRank" value="3" /> - <param name="MonoisotopeAdjustmentSet" value="[-1,2]" /> - <param name="UseSmartPlusThreeModel" value="false" /> - <output name="output" file="201208-378803-mm.pepXML" lines_diff="14" /> - </test> - <test> - <param name="input" value="input/201208-378803.mzML" /> - <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" /> <param name="CleavageRules" value="Trypsin" /> <param name="DecoyPrefix" value="XXX_" /> - <param name="common_fixed_modifications" value="" /> - <param name="common_variable_modifications" value="" /> <param name="PrecursorMzToleranceRule" value="mono" /> <param name="MonoPrecursorMzTolerance" value="15" /> <param name="MinTerminiCleavages" value="2" />