Mercurial > repos > galaxyp > msgfplus
diff msgfplus.xml @ 0:ee56530a559f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit bdb474693831a3375db79755e88641ad32b3b4e6
| author | galaxyp |
|---|---|
| date | Sun, 21 Feb 2016 11:04:06 -0500 |
| parents | |
| children | 797c755b9e74 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msgfplus.xml Sun Feb 21 11:04:06 2016 -0500 @@ -0,0 +1,265 @@ +<tool id="msgfplus" name="MS-GF+" version="0.1"> + <description> + Identifies peptides in tandem mass spectra using the MS-GF+ search engine. + </description> + <requirements> + <requirement type="package" version="10089">msgfplus</requirement> + <environment_variable name="LC_ALL" action="set_to">C</environment_variable> + </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[ + #set $db_name = $d.display_name.replace(".fasta", "") + ".fasta" + #set $input_name = $s.display_name + #set $output_name = $input_name.replace(".mzML", "") + ".mzid" + ln -s '$s' '${input_name}' && + ln -s '$d' '${db_name}' && + + 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 $custom_mods + echo '${mod.formula_or_mass},${mod.aa_specificity},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt && + #end for + + msgfjar=\$(which MSGFPlus.jar) && + ( [ -f "\$msgfjar" ] || (echo MSGFPlus.jar not found && exit 1)) && + + java -jar \$msgfjar + -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 $advanced.addFeatures + && + mv '$output_name' output +]]> + </command> + <inputs> + <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"/> + <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" /> + </outputs> + <tests> + <test> + <param name="s" value="input/201208-378803.mzML" /> + <param name="d" value="input/cow.protein.PRG2012-subset.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-50ppm-semitryptic-no_mods.mzid" lines_diff="6" /> + </test> + <test> + <param name="s" value="input/201208-378803.mzML" /> + <param name="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="CS" /> + <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" file="201208-378803-msgf-2mmu-tryptic-many_mods.mzid" lines_diff="6" /> + </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>