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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 |
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<tool id="msgfplus" name="MS-GF+" version="0.3.1"> <description> Identifies peptides in tandem mass spectra using the MS-GF+ search engine. </description> <requirements> <requirement type="package" version="2016.10.26">msgf_plus</requirement> </requirements> <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"/> </stdio> <command> <![CDATA[ #if $msgf_input.intype_selector == "single" #set $db_name = $msgf_input.d.element_identifier.replace(".fasta", "") + ".fasta" #set $input_name = $msgf_input.s.element_identifier.replace(".mzML", "") + ".mzML" ln -s '$msgf_input.s' '${input_name}' && ln -s '$msgf_input.d' '${db_name}' && #else if $msgf_input.intype_selector == "fractions" #set $db_name = $msgf_input.db_spectra.reverse.element_identifier.replace(".fasta", "") + ".fasta" #set $input_name = $msgf_input.db_spectra.name.replace(".mzML", "") + ".mzML" ln -s '$msgf_input.db_spectra.forward' '${input_name}' && ln -s '$msgf_input.db_spectra.reverse' '${db_name}' && #end if #set $output_name = $input_name.replace(".mzML", ".mzid") echo \\#Mods > Mods.txt && #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications) #for $mod in $common_mods.split(",") echo '$mod.replace("_", ",")' >> Mods.txt && #end for #for $mod in $custom_mods #set aa_nocomma = str($mod.aa_specificity).replace(",", "") echo '${mod.formula_or_mass},${aa_nocomma},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt && #end for msgf_plus -s '$input_name' -d '$db_name' -thread \${GALAXY_SLOTS:-1} -mod Mods.txt -tda $tda -t $t$precursor_ion_tol_units -ti $advanced.isotope_low,$advanced.isotope_high -m $advanced.m -inst $inst -e $e -protocol $advanced.protocol -ntt $ntt -minLength $advanced.minLength -maxLength $advanced.maxLength -minCharge $advanced.minCharge -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 && 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> </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" /> <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/> <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments"> <option value="ppm" selected="true">Parts per million (ppm)</option> <option value="Da">Daltons</option> </param> <param argument="-inst" label="Instrument type" type="select" help="The instrument type that generated the MS/MS spectra is used to determine the scoring model"> <option value="0" selected="true">Low-res (LCQ/LTQ)</option> <option value="1" >High-res (LTQ-Orbitrap)</option> <option value="2" >Q-TOF</option> <option value="3" >Q-Exactive</option> </param> <param argument="-e" type="select" label="Enzyme" help="Enzyme used to digest proteins in sample preparation; trypsin is the most commonly used enzyme"> <option value="0">Unspecific cleavage</option> <option value="1" selected="true">Trypsin, no P rule</option> <option value="2">Chymotrypsin, no P rule (FYWL)</option> <option value="3">Lys-C, no P rule</option> <option value="4">Lys-N</option> <option value="5">Glu-C (glutamyl endopeptidase)</option> <option value="6">Arg-C</option> <option value="7">Asp-N</option> <option value="8">Alpha-lytic protease</option> <option value="9">No enzyme</option> </param> <param argument="-ntt" type="select" format="text" label="Number of tolerable termini" help="Semi-specific requires more time than fully specific; non-specific requires much more."> <option value="2" selected="true">Fully specific (both termini match cleavage rules)</option> <option value="1">Semi-specific (at least one terminus must match cleavage rules)</option> <option value="0">Non-specific (neither terminus is required to match cleavage rules)</option> </param> <param name="common_fixed_modifications" type="select" label="Common Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> <option value="C2H3N1O1_C_fix_any_Carbamidomethyl" selected="true">Carbamidomethyl C</option> <option value="144.102063_*_fix_N-term_iTRAQ4plex">iTRAQ 4-plex N-term</option> <option value="144.102063_K_fix_any_iTRAQ4plex">iTRAQ 4-plex K</option> <option value="225.155833_*_fix_N-term_TMT6plex">TMT 2-plex N-term</option> <option value="225.155833_K_fix_any_TMT6plex">TMT 2-plex K</option> <option value="229.162932_*_fix_N-term_TMT6plex">TMT 6-or-10-plex N-term</option> <option value="229.162932_K_fix_any_TMT6plex">TMT 6-or-10-plex K</option> <sanitizer invalid_char=""><valid initial="string.printable"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer> </param> <param name="common_variable_modifications" type="select" label="Common 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"> <option value="C2H2O1_K_opt_any_Acetyl">Acetylation K</option> <option value="C2H2O_*_opt_Prot-N-term_Acetyl">Acetylation Protein N-term</option> <option value="C2H3NO_C_opt_any_Carbamidomethyl">Carbamidomethyl C</option> <option value="C2H3NO_*_opt_N-term_Carbamidomethyl">Carbamidomethyl N-term</option> <option value="H-1N-1O1_N_opt_any_Deamidated">Deamidation N</option> <option value="H-1N-1O1_Q_opt_any_Deamidated">Deamidation Q</option> <option value="CH2_K_opt_any_Methyl">Methylation K</option> <option value="O1_M_opt_any_Oxidation" selected="true">Oxidation M</option> <option value="HO3P_S_opt_any_Phospho">Phosphorylation S</option> <option value="HO3P_T_opt_any_Phospho">Phosphorylation T</option> <option value="HO3P_Y_opt_any_Phospho">Phosphorylation Y</option> <option value="H-2O-1_E_opt_N-term_Glu->pyro-Glu">Pyro-glu from E</option> <option value="H-3N-1_Q_opt_N-term_Gln->pyro-Glu">Pyro-glu from Q</option> <sanitizer invalid_char=""><valid initial="string.printable"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer> </param> <repeat name="custom_mods" title="Custom Modifications" help="Specify modifications with custom parameters"> <param name="formula_or_mass" type="text" label="Formula or Mass"> <sanitizer> <valid initial="string.digits"> <add value="C"/> <add value="H"/> <add value="O"/> <add value="N"/> <add value="S"/> <add value="P"/> <add value="B"/><add value="r"/> <add value="C"/><add value="l"/> <add value="F"/><add value="e"/> <add value="S"/> <add value="."/> <add value="-"/> </valid> </sanitizer> </param> <param name="aa_specificity" type="select" multiple="true" label="Amino Acid Specificity"> <option value="*" selected="true">Any</option> <option value="A">A</option> <option value="C">C</option> <option value="D">D</option> <option value="E">E</option> <option value="F">F</option> <option value="G">G</option> <option value="H">H</option> <option value="I">I</option> <option value="K">K</option> <option value="L">L</option> <option value="M">M</option> <option value="N">N</option> <option value="P">P</option> <option value="Q">Q</option> <option value="R">R</option> <option value="S">S</option> <option value="T">T</option> <option value="V">V</option> <option value="W">W</option> <option value="Y">Y</option> </param> <param name="fix_or_opt" type="select" label="Variable or Fixed?"> <option value="opt" selected="true">Variable</option> <option value="fix">Fixed</option> </param> <param name="position_specificity" type="select" label="Positional Specificity"> <option value="any" selected="true">Any</option> <option value="n-term">Peptide N-terminal</option> <option value="c-term">Peptide C-terminal</option> <option value="prot-n-term">Protein N-terminal</option> <option value="prot-c-term">Protein C-terminal</option> </param> <param name="mod_name" type="text" label="Name" help="If this mod has an entry there in Unimod, this name should match its name there" /> </repeat> <!-- MS-GF+ ADVANCED PARAMETERS --> <section name="advanced" title="Advanced Options"> <param argument="-minCharge" label="Minimum precursor charge" value="2" type="integer" help="Minimum precursor charge to consider if charges are not specified in the spectrum file"/> <param argument="-maxCharge" label="Maximum precursor charge" value="3" type="integer" help="Maximum precursor charge to consider if charges are not specified in the spectrum file"/> <param argument="-minLength" label="Minimum peptide length" value="6" type="integer" help="Minimum peptide length to consider"/> <param argument="-maxLength" label="Maximum peptide length" value="40" type="integer" help="Maximum peptide length to consider"/> <param name="num_ptms" label="Maximum modifications allowed per peptide" type="integer" value="2" /> <param argument="-m" label="Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)"> <option value="0" selected="True">As written in the spectrum or CID if no info</option> <option value="1" >CID</option> <option value="2" >ETD</option> <option value="3" >HCD</option> </param> <param argument="-protocol" label="Protocol type" type="select" help="Protocols are used to enable scoring parameters for enriched and/or labeled samples"> <option value="0" selected="True">Automatic</option> <option value="1" >Phosphorylation</option> <option value="2" >iTRAQ</option> <option value="3" >iTRAQPhospho</option> <option value="4" >TMT</option> <option value="5" >Standard</option> </param> <param argument="-n" label="Maximum matches per spectrum" type="integer" value="1" help="Number of peptide matches per spectrum to report" /> <param argument="-addFeatures" label="Calculate additional scoring features?" type="boolean" truevalue="1" falsevalue="0" help="If true, several extra derivative scores are calculated for each match" /> <param name="isotope_low" label="Lower isotope error range" type="integer" value="0" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation (-ti)" /> <param name="isotope_high" label="Upper isotope error range" type="integer" value="1" /> </section> </inputs> <outputs> <data name="output" format="mzid" from_work_dir="output" /> <data name="tsvoutput" format="tabular" from_work_dir="output.tsv" > <filter>tsvcheck</filter> </data> </outputs> <tests> <test> <param name="msgf_input|intype_selector" value="single" /> <param name="msgf_input|s" value="input/201208-378803.mzML" ftype="mzml" /> <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" ftype="fasta" /> <param name="tda" value="1" /> <param name="ntt" value="1" /> <param name="t" value="50" /> <param name="precursor_ion_tol_units" value="ppm" /> <param name="common_fixed_modifications" value="" /> <param name="common_variable_modifications" value="" /> <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" /> </test> <test> <param name="msgf_input|intype_selector" value="single" /> <param name="msgf_input|s" value="input/201208-378803.mzML" /> <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" /> <param name="tsvcheck" value="true" /> <param name="tda" value="1" /> <param name="ntt" value="1" /> <param name="t" value="50" /> <param name="precursor_ion_tol_units" value="ppm" /> <param name="common_fixed_modifications" value="" /> <param name="common_variable_modifications" value="" /> <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" /> <output name="tsvoutput" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.tsv" compare="sim_size" delta="20" /> </test> <test> <param name="msgf_input|intype_selector" value="fractions" /> <param name="msgf_input|db_spectra"> <collection type="paired"> <element name="forward" value="input/201208-378803.mzML" /> <element name="reverse" value="input/cow.protein.PRG2012-subset.fasta" /> </collection> </param> <param name="tda" value="1" /> <param name="ntt" value="1" /> <param name="t" value="50" /> <param name="precursor_ion_tol_units" value="ppm" /> <param name="common_fixed_modifications" value="" /> <param name="common_variable_modifications" value="" /> <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="100" /> </test> <test> <param name="msgf_input|intype_selector" value="single" /> <param name="msgf_input|s" value="input/201208-378803.mzML" /> <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" /> <param name="tda" value="1" /> <param name="t" value="0.02" /> <param name="precursor_ion_tol_units" value="Da" /> <param name="isotope_low" value="-1" /> <param name="isotope_high" value="0" /> <param name="m" value="3" /> <param name="inst" value="2" /> <param name="e" value="3" /> <param name="protocol" value="2" /> <param name="minLength" value="10" /> <param name="maxLength" value="20" /> <param name="minCharge" value="2" /> <param name="maxCharge" value="6" /> <param name="n" value="2" /> <param name="addFeatures" value="1" /> <param name="common_fixed_modifications" value="C2H3N1O1_C_fix_any_Carbamidomethyl,144.102063_*_fix_N-term_iTRAQ4plex,144.102063_K_fix_any_iTRAQ4plex" /> <param name="common_variable_modifications" value="O1_M_opt_any_Oxidation,H-3N-1_Q_opt_N-term_Gln->pyro-Glu" /> <param name="custom_mods_0|formula_or_mass" value="C-2H-2O-2" /> <param name="custom_mods_0|aa_specificity" value="G" /> <param name="custom_mods_0|fix_or_opt" value="opt" /> <param name="custom_mods_0|position_specificity" value="c-term" /> <param name="custom_mods_0|mod_name" value="Gly-loss+Amide" /> <param name="custom_mods_1|formula_or_mass" value="C10H10N5O7P" /> <param name="custom_mods_1|aa_specificity" value="C,S" /> <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"> <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> **What it does** Performs protein identification via database search using MS-GF+. </help> <citations> <citation type="doi">10.1038/ncomms6277</citation> <citation type="doi">10.1021/pr8001244</citation> <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Gruening, B, Chambers, MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" --> </citations> </tool>