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view msgfplus_search.xml @ 16:66a149ef79f7 draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author | iracooke |
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date | Tue, 20 Oct 2015 20:01:47 -0400 |
parents | 6c751c59ce18 |
children | 7990ee72821b |
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<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0"> <description>Run an MSGF+ Search</description> <requirements> <container type="docker">iracooke/protk-1.4.3</container> <requirement type="package" version="1.4.3">protk</requirement> <requirement type="package" version="20140210">msgfplus</requirement> <requirement type="package" version="3_0_4388">proteowizard</requirement> </requirements> <command> msgfplus_search.rb #if $database.source_select=="built_in": --galaxy -d $database.dbkey #else --galaxy -d $database.fasta_file #end if --var-mods=' $variable_mods #for $custom_variable_mod in $custom_variable_mods: ,${custom_variable_mod.custom_mod} #end for ' --fix-mods=' $fixed_mods #for $custom_fix_mod in $custom_fix_mods: ,${custom_fix_mod.custom_mod} #end for ' $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages $cleavage_semi -p $precursor_ion_tol --instrument=$instrument --isotope-error-range=$isotope_error_range --fragment-method=$fragment_method --protocol=$protocol --min-pep-len=$min_pep_len --max-pep-len=$max_pep_len --max-pep-charge=$max_pep_charge --min-pep-charge=$min_pep_charge --num-reported-matches=$num_reported_matches --java-mem=$java_mem --threads "\${GALAXY_SLOTS:-12}" #if $pepxml_output_use: --pepxml #end if </command> <inputs> <conditional name="database"> <param name="source_select" type="select" label="Database source"> <option value="built_in">Built-In</option> <option value="input_ref" selected="true">Your Upload File</option> </param> <when value="built_in"> <param name="dbkey" type="select" format="text" > <label>Database</label> <options from_file="pepxml_databases.loc"> <column name="name" index="0" /> <column name="value" index="2" /> </options> </param> </when> <when value="input_ref"> <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> </when> </conditional> <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/> <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed"> <options from_file="msgfplus_mods_var.loc"> <column name="name" index="0" /> <column name="value" index="2" /> </options> </param> <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these"> <param name="custom_mod" type="text" /> </repeat> <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed"> <options from_file="msgfplus_mods_fix.loc"> <column name="name" index="0" /> <column name="value" index="2" /> </options> </param> <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these"> <param name="custom_mod" type="text"> </param> </repeat> <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites"> <label>Missed Cleavages Allowed</label> <option value="0">0</option> <option value="1">1</option> <option selected="true" value="2">2</option> </param> <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue="" /> <param name="enzyme" type="select" format="text"> <label>Enzyme</label> <option value="0">unspecific cleavage</option> <option value="1" selected="true">Trypsin</option> <option value="2">Chymotrypsin</option> <option value="3">Lys-C</option> <option value="4">Lys-N</option> <option value="5">glutamyl endopeptidase</option> <option value="6">Arg-C</option> <option value="7">Asp-N</option> <option value="8">alphaLP</option> <option value="9">no cleavage</option> </param> <param name="instrument" type="select" format="text"> <label>Instrument Type</label> <option value="2">TOF</option> <option value="0" selected="true">Low-res LCQ/LTQ</option> <option value="1">High-res LTQ</option> </param> <param name="fragment_method" type="select" format="text"> <label>Fragmentation Method</label> <option value="0">Respect Input File</option> <option value="1">CID</option> <option value="2">ETD</option> <option value="3">HCD</option> <option value="4">Merge spectra from same precursor</option> </param> <param name="protocol" type="select" format="text"> <label>Protocol</label> <option value="0">NoProtocol</option> <option value="1">Phosphorylation</option> <option value="2">iTRAQ</option> <option value="3">iTRAQPhospho</option> </param> <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/> <param name="precursor_tolu" type="select" format="text"> <label>Precursor Ion Tolerance Units</label> <option value="ppm">ppm</option> <option value="Da">Da</option> </param> <param name="isotope_error_range" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation." type="text" size="80" value="0,1" label="Isotope Error Range"/> <param name="min_pep_len" help="" type="integer" value="6" label="Minimum Peptide Length"/> <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/> <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/> <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/> <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/> <param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/> <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" /> </inputs> <outputs> <data format="mzid" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.${'pepXML' if $pepxml_output_use else 'mzid'}"> <change_format> <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file"/> </change_format> </data> </outputs> <tests> <!-- Just test that the tool runs and produces vaguely correct output --> <test> <param name="source_select" value="input_ref"/> <param name="fasta_file" value="testdb.fasta" format="fasta"/> <param name="input_file" value="tiny.mzML" format="mzml"/> <param name="precursor_ion_tol" value="200"/> <param name="pepxml_output_use" value="true"/> <output name="output" format="raw_pepxml"> <assert_contents> <has_text text="FALPQYLKTVYQHQKAMKPWIQPKTKVIPYVRYL" /> </assert_contents> </output> </test> </tests> <help> **What it does** Runs an MS/MS database search using the MSGFPlus search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores. ---- **References** Please see http://proteomics.ucsd.edu/Software/MSGFPlus.html for details of the MSGFPlus search engine and references describing its algorithm </help> </tool>