Mercurial > repos > bgruening > openms
view IDFilter.xml @ 4:6ead64a594bd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
| author | bgruening |
|---|---|
| date | Wed, 27 Jan 2016 10:06:49 -0500 |
| parents | 3d84209d3178 |
| children |
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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="IDFilter" name="IDFilter" version="2.0.0"> <description>Filters results from protein or peptide identification engines based on different criteria.</description> <macros> <token name="@EXECUTABLE@">IDFilter</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>IDFilter #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if #if $param_min_length: -min_length $param_min_length #end if #if $param_max_length: -max_length $param_max_length #end if #if $param_min_charge: -min_charge $param_min_charge #end if #if $param_var_mods: -var_mods #end if #if $param_unique: -unique #end if #if $param_unique_per_protein: -unique_per_protein #end if #if $param_keep_unreferenced_protein_hits: -keep_unreferenced_protein_hits #end if #if $param_remove_decoys: -remove_decoys #end if #if $param_delete_unreferenced_peptide_hits: -delete_unreferenced_peptide_hits #end if -threads \${GALAXY_SLOTS:-24} #if $param_precursor_rt: -precursor:rt "$param_precursor_rt" #end if #if $param_precursor_mz: -precursor:mz "$param_precursor_mz" #end if #if $param_precursor_allow_missing: -precursor:allow_missing #end if #if $param_score_pep: -score:pep $param_score_pep #end if #if $param_score_prot: -score:prot $param_score_prot #end if #if $param_thresh_pep: -thresh:pep $param_thresh_pep #end if #if $param_thresh_prot: -thresh:prot $param_thresh_prot #end if #if $param_whitelist_proteins: -whitelist:proteins $param_whitelist_proteins #end if #if $param_whitelist_by_seq_only: -whitelist:by_seq_only #end if #if $rep_param_whitelist_protein_accessions: -whitelist:protein_accessions #for token in $rep_param_whitelist_protein_accessions: #if " " in str(token): "$token.param_whitelist_protein_accessions" #else $token.param_whitelist_protein_accessions #end if #end for #end if #if $param_blacklist_peptides: -blacklist:peptides $param_blacklist_peptides #end if #if $param_blacklist_ignore_modifications: -blacklist:ignore_modifications #end if #if $param_rt_p_value: -rt:p_value $param_rt_p_value #end if #if $param_rt_p_value_1st_dim: -rt:p_value_1st_dim $param_rt_p_value_1st_dim #end if #if $param_mz_error: -mz:error $param_mz_error #end if #if $param_mz_unit: -mz:unit #if " " in str($param_mz_unit): "$param_mz_unit" #else $param_mz_unit #end if #end if #if $param_best_n_peptide_hits: -best:n_peptide_hits $param_best_n_peptide_hits #end if #if $param_best_n_protein_hits: -best:n_protein_hits $param_best_n_protein_hits #end if #if $param_best_strict: -best:strict #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #if $adv_opts.param_best_n_to_m_peptide_hits: -best:n_to_m_peptide_hits "$adv_opts.param_best_n_to_m_peptide_hits" #end if #end if </command> <inputs> <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/> <param help="(-min_length) Value 0 will have no filter effect" label="Keep only peptide hits with a length greater or equal this value" min="0" name="param_min_length" optional="True" type="integer" value="0"/> <param help="(-max_length) Value 0 will have no filter effect. Value is overridden by min_length, i.e. if max_length < min_length, max_length will be ignored" label="Keep only peptide hits with a length less or equal this value" min="0" name="param_max_length" optional="True" type="integer" value="0"/> <param help="(-min_charge) " label="Keep only peptide hits for tandem spectra with charge greater or equal this value" min="1" name="param_min_charge" optional="True" type="integer" value="1"/> <param checked="false" falsevalue="" help="(-var_mods) " label="Keep only peptide hits with variable modifications (fixed modifications from SearchParameters will be ignored)" name="param_var_mods" optional="True" truevalue="-var_mods" type="boolean"/> <param checked="false" falsevalue="" help="(-unique) " label="If a peptide hit occurs more than once per PSM, only one instance is kept" name="param_unique" optional="True" truevalue="-unique" type="boolean"/> <param checked="false" falsevalue="" help="(-unique_per_protein) Remember that isoforms count as different proteins!" label="Only peptides matching exactly one protein are kept" name="param_unique_per_protein" optional="True" truevalue="-unique_per_protein" type="boolean"/> <param checked="false" falsevalue="" help="(-keep_unreferenced_protein_hits) " label="Proteins not referenced by a peptide are retained in the ids" name="param_keep_unreferenced_protein_hits" optional="True" truevalue="-keep_unreferenced_protein_hits" type="boolean"/> <param checked="false" falsevalue="" help="(-remove_decoys) Usually used in combination with 'delete_unreferenced_peptide_hits'" label="Remove proteins according to the information in the user parameters" name="param_remove_decoys" optional="True" truevalue="-remove_decoys" type="boolean"/> <param checked="false" falsevalue="" help="(-delete_unreferenced_peptide_hits) Usually used in combination with 'score:prot' or 'thresh:prot'" label="Peptides not referenced by any protein are deleted in the ids" name="param_delete_unreferenced_peptide_hits" optional="True" truevalue="-delete_unreferenced_peptide_hits" type="boolean"/> <param help="(-rt) " label="Retention time range to extract" name="param_precursor_rt" size="30" type="text" value=":"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param help="(-mz) " label="Mass-to-charge range to extract" name="param_precursor_mz" size="30" type="text" value=":"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param checked="false" falsevalue="" help="(-allow_missing) " label="When filtering by precursor RT or m/z, keep peptide IDs with missing precursor information ('RT'/'MZ' meta values)?" name="param_precursor_allow_missing" optional="True" truevalue="-precursor:allow_missing" type="boolean"/> <param help="(-pep) The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc" label="The score which should be reached by a peptide hit to be kept" name="param_score_pep" type="float" value="0.0"/> <param help="(-prot) Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides" label="The score which should be reached by a protein hit to be kept" name="param_score_prot" type="float" value="0.0"/> <param help="(-pep) " label="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold" name="param_thresh_pep" type="float" value="0.0"/> <param help="(-prot) Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides" label="Keep a protein hit only if its score is above this fraction of the protein significance threshold" name="param_thresh_prot" type="float" value="0.0"/> <param format="fasta" help="(-proteins) <br>All peptides that are not a substring of a sequence in this file are removed <br>All proteins whose accession is not present in this file are removed" label="filename of a FASTA file containing protein sequences" name="param_whitelist_proteins" optional="True" type="data"/> <param checked="false" falsevalue="" help="(-by_seq_only) " label="Match peptides with FASTA file by sequence instead of accession and disable protein filtering" name="param_whitelist_by_seq_only" optional="True" truevalue="-whitelist:by_seq_only" type="boolean"/> <repeat min="0" name="rep_param_whitelist_protein_accessions" title="param_whitelist_protein_accessions"> <param help="(-protein_accessions) <br>Only proteins of the provided list are retained" label="All peptides that are not referencing at least one of the provided protein accession are removed" name="param_whitelist_protein_accessions" size="30" type="text"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <param format="xml" help="(-peptides) Use with blacklist:ignore_modification flag to only compare by sequence. <br>" label="Peptides having the same sequence and modification assignment as any peptide in this file will be filtered out" name="param_blacklist_peptides" optional="True" type="data"/> <param checked="false" falsevalue="" help="(-ignore_modifications) <br>" label="Compare blacklisted peptides by sequence only" name="param_blacklist_ignore_modifications" optional="True" truevalue="-blacklist:ignore_modifications" type="boolean"/> <param help="(-p_value) " label="Retention time filtering by the p-value predicted by RTPredict" max="1.0" min="0.0" name="param_rt_p_value" optional="True" type="float" value="0.0"/> <param help="(-p_value_1st_dim) " label="Retention time filtering by the p-value predicted by RTPredict for first dimension" max="1.0" min="0.0" name="param_rt_p_value_1st_dim" optional="True" type="float" value="0.0"/> <param help="(-error) " label="Filtering by deviation to theoretical mass (disabled for negative values)" name="param_mz_error" type="float" value="-1.0"/> <param help="(-unit) " label="Absolute or relative erro" name="param_mz_unit" optional="True" type="select" value="ppm"> <option value="Da">Da</option> <option value="ppm">ppm</option> </param> <param help="(-n_peptide_hits) " label="Keep only the 'n' highest scoring peptide hits per spectrum (for n>0)" min="0" name="param_best_n_peptide_hits" optional="True" type="integer" value="0"/> <param help="(-n_protein_hits) " label="Keep only the 'n' highest scoring protein hits (for n>0)" min="0" name="param_best_n_protein_hits" optional="True" type="integer" value="0"/> <param checked="false" falsevalue="" help="(-strict) <br>Similar to n_peptide_hits=1, but if there are two or more highest scoring hits, none are kept" label="Keep only the highest scoring peptide hit" name="param_best_strict" optional="True" truevalue="-best:strict" type="boolean"/> <expand macro="advanced_options"> <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> <param help="(-n_to_m_peptide_hits) " label="peptide hit rank range to extracts" name="param_best_n_to_m_peptide_hits" size="30" type="text" value=":"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </expand> </inputs> <outputs> <data format="xml" name="param_out"/> </outputs> <help>Filters results from protein or peptide identification engines based on different criteria. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFilter.html</help> </tool>