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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
| author | bgruening |
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| date | Wed, 27 Jan 2016 10:06:49 -0500 |
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<?xml version="1.0" encoding="UTF-8"?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> <!--Proposed Tool Section: [ID Processing]--> <tool id="PeptideIndexer" name="PeptideIndexer" version="2.0.0"> <description>Refreshes the protein references for all peptide hits.</description> <macros> <token name="@EXECUTABLE@">PeptideIndexer</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>PeptideIndexer #if $param_in: -in $param_in #end if #if $param_fasta: -fasta $param_fasta #end if #if $param_out: -out $param_out #end if #if $param_decoy_string: -decoy_string "$param_decoy_string" #end if #if $param_prefix: -prefix #end if #if $param_missing_decoy_action: -missing_decoy_action #if " " in str($param_missing_decoy_action): "$param_missing_decoy_action" #else $param_missing_decoy_action #end if #end if #if $param_write_protein_sequence: -write_protein_sequence #end if #if $param_write_protein_description: -write_protein_description #end if #if $param_keep_unreferenced_proteins: -keep_unreferenced_proteins #end if #if $param_allow_unmatched: -allow_unmatched #end if #if $param_full_tolerant_search: -full_tolerant_search #end if #if $param_aaa_max: -aaa_max $param_aaa_max #end if #if $param_mismatches_max: -mismatches_max $param_mismatches_max #end if #if $param_IL_equivalent: -IL_equivalent #end if -threads \${GALAXY_SLOTS:-24} #if $param_enzyme_name: -enzyme:name #if " " in str($param_enzyme_name): "$param_enzyme_name" #else $param_enzyme_name #end if #end if #if $param_enzyme_specificity: -enzyme:specificity #if " " in str($param_enzyme_specificity): "$param_enzyme_specificity" #else $param_enzyme_specificity #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #end if </command> <inputs> <param format="xml" help="(-in) " label="Input idXML file containing the identifications" name="param_in" optional="False" type="data"/> <param format="fasta" help="(-fasta) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'" label="Input sequence database in FASTA format" name="param_fasta" optional="False" type="data"/> <param help="(-decoy_string) " label="String that was appended (or prefixed - see 'prefix' flag below) to the accessions in the protein database to indicate decoy proteins" name="param_decoy_string" size="30" type="text" value="_rev"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param checked="false" falsevalue="" help="(-prefix) " label="If set, protein accessions in the database contain 'decoy_string' as prefix" name="param_prefix" optional="True" truevalue="-prefix" type="boolean"/> <param help="(-missing_decoy_action) " label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message)" name="param_missing_decoy_action" optional="True" type="select" value="error"> <option value="error">error</option> <option value="warn">warn</option> </param> <param checked="false" falsevalue="" help="(-write_protein_sequence) " label="If set, the protein sequences are stored as well" name="param_write_protein_sequence" optional="True" truevalue="-write_protein_sequence" type="boolean"/> <param checked="false" falsevalue="" help="(-write_protein_description) " label="If set, the protein description is stored as well" name="param_write_protein_description" optional="True" truevalue="-write_protein_description" type="boolean"/> <param checked="false" falsevalue="" help="(-keep_unreferenced_proteins) " label="If set, protein hits which are not referenced by any peptide are kept" name="param_keep_unreferenced_proteins" optional="True" truevalue="-keep_unreferenced_proteins" type="boolean"/> <param checked="false" falsevalue="" help="(-allow_unmatched) By default (i.e. if this flag is not set) the program terminates with an error on unmatched peptides" label="If set, unmatched peptide sequences are allowed" name="param_allow_unmatched" optional="True" truevalue="-allow_unmatched" type="boolean"/> <param checked="false" falsevalue="" help="(-full_tolerant_search) Thus potentially more proteins (containing ambiguous amino acids) are associated. This is much slower!" label="If set, all peptide sequences are matched using tolerant search" name="param_full_tolerant_search" optional="True" truevalue="-full_tolerant_search" type="boolean"/> <param help="(-aaa_max) AAA's are 'B', 'Z' and 'X'" label="[tolerant search only] Maximal number of ambiguous amino acids (AAA) allowed when matching to a protein database with AAA's" min="0" name="param_aaa_max" optional="True" type="integer" value="4"/> <param help="(-mismatches_max) In general this param should only be changed if you want to look for other potential origins of a peptide which might have unknown SNPs or alike" label="[tolerant search only] Maximal number of real mismatches (will be used after checking for ambiguous AA's (see 'aaa_max' option)" min="0" name="param_mismatches_max" optional="True" type="integer" value="0"/> <param checked="false" falsevalue="" help="(-IL_equivalent) " label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" name="param_IL_equivalent" optional="True" truevalue="-IL_equivalent" type="boolean"/> <param help="(-name) e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)" label="Enzyme which determines valid cleavage sites -" name="param_enzyme_name" optional="True" type="select" value="Trypsin"> <option value="Chymotrypsin">Chymotrypsin</option> <option value="V8-DE">V8-DE</option> <option value="2-iodobenzoate">2-iodobenzoate</option> <option value="Lys-C/P">Lys-C/P</option> <option value="PepsinA">PepsinA</option> <option value="Lys-C">Lys-C</option> <option value="Trypsin">Trypsin</option> <option value="Asp-N_ambic">Asp-N_ambic</option> <option value="no cleavage">no cleavage</option> <option value="CNBr">CNBr</option> <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> <option value="unspecific cleavage">unspecific cleavage</option> <option value="proline endopeptidase">proline endopeptidase</option> <option value="TrypChymo">TrypChymo</option> <option value="Trypsin/P">Trypsin/P</option> <option value="Arg-C">Arg-C</option> <option value="Formic_acid">Formic_acid</option> <option value="V8-E">V8-E</option> <option value="leukocyte elastase">leukocyte elastase</option> <option value="Asp-N">Asp-N</option> </param> <param help="(-specificity) <br> 'full': both internal cleavage sites must match. <br> 'semi': one of two internal cleavage sites must match. <br> 'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here" label="Specificity of the enzyme" name="param_enzyme_specificity" optional="True" type="select" value="full"> <option value="full">full</option> <option value="semi">semi</option> <option value="none">none</option> </param> <expand macro="advanced_options"> <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> </expand> </inputs> <outputs> <data format="xml" name="param_out"/> </outputs> <help>Refreshes the protein references for all peptide hits. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeptideIndexer.html</help> </tool>