Mercurial > repos > galaxyp > peptideshaker
view macros.xml @ 36:bced7eb9e197 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc8de3ad970c292f4b5d493194a333dcac823fb
author | galaxyp |
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date | Mon, 27 Feb 2017 14:29:05 -0500 |
parents | 0ebf3d3e4c90 |
children | 7f2aeb19650f |
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<macros> <xml name="stdio"> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> <regex match="java.*Exception" level="fatal" description="Java Exception"/> <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> <regex match="CompomicsError" level="fatal" description="Compomics Error"/> </stdio> </xml> <token name="@GENERAL_PARAMETERS@"> -frag_tol "${precursor_options.fragment_tol}" ### -frag_ppm -prec_tol "${precursor_options.precursor_ion_tol}" -prec_ppm "${precursor_options.precursor_ion_tol_units}" -min_charge $precursor_options.min_charge -max_charge $precursor_options.max_charge -fi $precursor_options.forward_ion -ri $precursor_options.reverse_ion -min_isotope ${precursor_options.min_isotope} -max_isotope ${precursor_options.max_isotope} #if $protein_digest_options.digestion.cleavage == 'default': ## -enzyme "Trysin" -mc $protein_digest_options.digestion.missed_cleavages #elif $protein_digest_options.digestion.cleavage == '0' and len($protein_digest_options.digestion.digests) > 0: #set $enzymes = [] #set $missed_cleavages = [] ## #set $specificities = [] #for $i, $digest in enumerate($protein_digest_options.digestion.digests): #silent $enzymes.append(str($digest.enzyme)) #silent $missed_cleavages.append(str($digest.missed_cleavages)) ## #silent $specificities.append(str($digest.specificity)) #end for -enzyme "#echo ','.join($enzymes)#" -mc "#echo ','.join($missed_cleavages)#" ## -specificity "#echo ','.join($specificities)#" #else: -digestion $protein_digest_options.digestion.cleavage #end if #set $fixed_mods_str = $protein_modification_options.fixed_modifications or '' #set $variable_mods_str = $protein_modification_options.variable_modifications or '' #if $fixed_mods_str -fixed_mods "$fixed_mods_str" #end if #if $variable_mods_str -variable_mods "$variable_mods_str" #end if </token> <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> <token name="@SEARCHGUI_VERSION@">3.2.8</token> <xml name="general_options"> <section name="protein_digest_options" expanded="false" title="Protein Digestion Options"> <conditional name="digestion"> <param name="cleavage" type="select" label="Digestion"> <option value="default" selected="true">Trypsin</option> <option value="0">Select Enzymes</option> <option value="1">Unspecific Cleavage</option> <option value="2">Whole Protein</option> </param> <when value="default"> <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> </when> <when value="0"> <repeat name="digests" min="1" title="Enzymes"> <param name="enzyme" type="select" label="Enzyme" help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> <option value="Trypsin">Trypsin</option> <option value="Arg-C">Arg-C</option> <option value="CNBr">CNBr</option> <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> <option value="Formic Acid">Formic Acid</option> <option value="Lys-C">Lys-C</option> <option value="Lys-C, no P rule">Lys-C, no P rule</option> <option value="Pepsin A">Pepsin A</option> <option value="Trypsin + CNBr">Trypsin + CNBr</option> <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> <option value="Trypsin, no P rule">Trypsin, no P rule</option> <option value="Whole Protein">Whole Protein</option> <option value="Asp-N">Asp-N</option> <option value="Glu-C">Glu-C</option> <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> <option value="Top-Down">Top-Down</option> <option value="Semi-Tryptic">Semi-Tryptic</option> <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! --> <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> <option value="Asp-N (DE)">Asp-N (DE)</option> <option value="Glu-C (DE)">Glu-C (DE)</option> <option value="Lys-N (K)">Lys-N (K)</option> <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> <option value="Semi-Glu-C">Semi-Glu-C</option> <option value="LysargiNase">LysargiNase</option> <option value="Semi-LysargiNase">Semi-LysargiNase</option> <option value="Trypsin + Glu-C">Trypsin + Glu-C</option> <option value="Semi-Arg-C">Semi-Arg-C</option> <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option> <option value="Arg-N">Arg-N</option> <option value="Semi-Arg-N">Semi-Arg-N</option> </param> <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> <!-- <param name="specificity" type="select" label="Specificity"> <option value="0" selected="true">Specific at both termini</option> <option value="1">Semi-Specific - one terminus</option> <option value="2">Specific at the N-terminus only</option> <option value="3">Specific at the C-terminus only</option> </param> --> </repeat> </when> <when value="1"/> <when value="2"/> </conditional> </section> <section name="precursor_options" expanded="false" title="Precursor Options"> <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> <option value="1">Parts per million (ppm)</option> <option value="2">Daltons</option> </param> <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" help="Provide error value for fragment ions, based on instrument used"/> <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> <option value="a">a</option> <option value="b" selected="true">b</option> <option value="c">c</option> </param> <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> <option value="x">x</option> <option value="y" selected="true">y</option> <option value="z">z</option> </param> <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" /> <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" /> </section> <section name="protein_modification_options" expanded="false" title="Protein Modification Options"> <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> <options from_file="searchgui_mods.loc"> <column name="name" index="0" /> <column name="value" index="0" /> </options> </param> <param name="variable_modifications" type="select" label="Variable 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"> <options from_file="searchgui_mods.loc"> <column name="name" index="0" /> <column name="value" index="0" /> </options> </param> </section> </xml> <xml name="citations"> <citations> <citation type="doi">10.1186/1471-2105-12-70</citation> <citation type="doi">10.1002/pmic.201000595</citation> <citation type="doi">doi:10.1038/nbt.3109</citation> </citations> </xml> </macros>