openms: IDFilter.xml comparison

comparison 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

comparison

equal deleted inserted replaced

-:ec62782f6c68
+:6ead64a594bd
-<?xml version='1.0' encoding='UTF-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
-<tool id="IDFilter" name="IDFilter" version="1.12.0">
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
-<description>Filters results from protein or peptide identification engines based on different criteria.</description>
+<!--Proposed Tool Section: [ID Processing]-->
-<macros>
+<tool id="IDFilter" name="IDFilter" version="2.0.0">
-<token name="@EXECUTABLE@">IDFilter</token>
+<description>Filters results from protein or peptide identification engines based on different criteria.</description>
-<import>macros.xml</import>
+<macros>
-</macros>
+<token name="@EXECUTABLE@">IDFilter</token>
-<expand macro="stdio"/>
+<import>macros.xml</import>
-<expand macro="requirements"/>
+</macros>
-<command>IDFilter
+<expand macro="references"/>
+<expand macro="stdio"/>
--in ${param_in}
+<expand macro="requirements"/>
--out ${param_out}
+<command>IDFilter
--min_length ${param_min_length}
--max_length ${param_max_length}
+#if $param_in:
--min_charge ${param_min_charge}
+-in $param_in
-${param_var_mods}
+#end if
-${param_unique}
+#if $param_out:
-${param_unique_per_protein}
+-out $param_out
-${param_keep_unreferenced_protein_hits}
+#end if
-${param_delete_unreferenced_peptide_hits}
+#if $param_min_length:
--threads \${GALAXY_SLOTS:-24}
+-min_length $param_min_length
--precursor:rt ${param_rt}
+#end if
--precursor:mz ${param_mz}
+#if $param_max_length:
-${param_allow_missing}
+-max_length $param_max_length
--score:pep ${param_pep}
+#end if
--score:prot ${param_prot}
+#if $param_min_charge:
--thresh:pep ${param_pep}
+-min_charge $param_min_charge
--thresh:prot ${param_prot}
+#end if
--whitelist:proteins ${param_proteins}
+#if $param_var_mods:
-${param_by_seq_only}
+-var_mods
--blacklist:peptides ${param_peptides}
+#end if
--rt:p_value ${param_p_value}
+#if $param_unique:
--rt:p_value_1st_dim ${param_p_value_1st_dim}
+-unique
--mz:error ${param_error}
+#end if
--mz:unit ${param_unit}
+#if $param_unique_per_protein:
--best:n_peptide_hits ${param_n_peptide_hits}
+-unique_per_protein
--best:n_protein_hits ${param_n_protein_hits}
+#end if
-${param_strict}
+#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 $param_precursor_rt:
+-precursor:rt     &quot;$param_precursor_rt&quot;
+#end if
+#if $param_precursor_mz:
+-precursor:mz     &quot;$param_precursor_mz&quot;
+#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 $rep_param_whitelist_protein_accessions:
+#if &quot; &quot; in str(token):
+&quot;$token.param_whitelist_protein_accessions&quot;
+#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 $param_mz_unit:
+-mz:unit
+#if &quot; &quot; in str($param_mz_unit):
+&quot;$param_mz_unit&quot;
+#else
+$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':
--best:n_to_m_peptide_hits ${adv_opts.param_n_to_m_peptide_hits}
+#if $adv_opts.param_force:
+-force
+#end if
+#if $adv_opts.param_best_n_to_m_peptide_hits:
+-best:n_to_m_peptide_hits     &quot;$adv_opts.param_best_n_to_m_peptide_hits&quot;
+#end if
 #end if
 </command>
 <inputs>
-<param name="param_in" type="data" format="idXML" optional="False" label="input file " help="(-in)"/>
+<param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
-<param name="param_min_length" type="integer" min="0" optional="True" value="0" label="Keep only peptide hits with a length greater or equal this value. Value 0 will have no filter effect." help="(-min_length)"/>
+<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 name="param_max_length" type="integer" max="0" optional="True" value="0" label="Keep only peptide hits with a length less or equal this value. Value 0 will have no filter effect. Value is overridden by min_length, i.e. if max_length &lt; min_length, max_length will be ignored." help="(-max_length)"/>
+<param help="(-max_length) Value 0 will have no filter effect. Value is overridden by min_length, i.e. if max_length &lt; 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 name="param_min_charge" type="integer" min="1" optional="True" value="1" label="Keep only peptide hits for tandem spectra with charge greater or equal this value." help="(-min_charge)"/>
+<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 name="param_var_mods" type="boolean" truevalue="-var_mods true" falsevalue="-var_mods false" checked="false" optional="True" label="Keep only peptide hits with variable modifications (fixed modifications from SearchParameters will be ignored)." help="(-var_mods)"/>
+<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 name="param_unique" type="boolean" truevalue="-unique true" falsevalue="-unique false" checked="false" optional="True" label="If a peptide hit occurs more than once per PSM, only one instance is kept." help="(-unique)"/>
+<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 name="param_unique_per_protein" type="boolean" truevalue="-unique_per_protein true" falsevalue="-unique_per_protein false" checked="false" optional="True" label="Only peptides matching exactly one protein are kept. Remember that isoforms count as different proteins!" help="(-unique_per_protein)"/>
+<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 name="param_keep_unreferenced_protein_hits" type="boolean" truevalue="-keep_unreferenced_protein_hits true" falsevalue="-keep_unreferenced_protein_hits false" checked="false" optional="True" label="Proteins not referenced by a peptide are retained in the idXML." help="(-keep_unreferenced_protein_hits)"/>
+<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 name="param_delete_unreferenced_peptide_hits" type="boolean" truevalue="-delete_unreferenced_peptide_hits true" falsevalue="-delete_unreferenced_peptide_hits false" checked="false" optional="True" label="Peptides not referenced by any protein are deleted in the idXML. Usually used in combination with 'score:prot' or 'thresh:prot'." help="(-delete_unreferenced_peptide_hits)"/>
+<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 name="param_rt" type="text" size="20" value=":" label="Retention time range to extract." help="(-rt)"/>
+<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 name="param_mz" type="text" size="20" value=":" label="Mass-to-charge range to extract." help="(-mz)"/>
+<param help="(-rt) " label="Retention time range to extract" name="param_precursor_rt" size="30" type="text" value=":">
-<param name="param_allow_missing" type="boolean" truevalue="-precursor:allow_missing true" falsevalue="-precursor:allow_missing false" checked="false" optional="True" label="When filtering by precursor RT or m/z, keep peptide IDs with missing precursor information ('RT'/'MZ' meta values)?" help="(-allow_missing)"/>
+<sanitizer>
-<param name="param_pep" type="float" value="0.0" label="The score which should be reached by a peptide hit to be kept. 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." help="(-pep)"/>
+<valid initial="string.printable">
-<param name="param_prot" type="float" value="0.0" label="The score which should be reached by a protein hit to be kept. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides." help="(-prot)"/>
+<remove value="'"/>
-<param name="param_pep" type="float" value="0.0" label="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." help="(-pep)"/>
+<remove value="&quot;"/>
-<param name="param_prot" type="float" value="0.0" label="Keep a protein hit only if its score is above this fraction of the protein significance threshold. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides." help="(-prot)"/>
+</valid>
-<param name="param_proteins" type="data" format="fasta" optional="True" label="filename of a FASTA file containing protein sequences.#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." help="(-proteins)"/>
+</sanitizer>
-<param name="param_by_seq_only" type="boolean" truevalue="-whitelist:by_seq_only true" falsevalue="-whitelist:by_seq_only false" checked="false" optional="True" label="Match peptides with FASTA file by sequence instead of accession and disable protein filtering." help="(-by_seq_only)"/>
+</param>
-<param name="param_peptides" type="data" format="idXML" optional="True" label="Peptides having the same sequence as any peptide in this file will be filtered out#br#" help="(-peptides)"/>
+<param help="(-mz) " label="Mass-to-charge range to extract" name="param_precursor_mz" size="30" type="text" value=":">
-<param name="param_p_value" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict." help="(-p_value)"/>
+<sanitizer>
-<param name="param_p_value_1st_dim" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Retention time filtering by the p-value predicted by RTPredict for first dimension." help="(-p_value_1st_dim)"/>
+<valid initial="string.printable">
-<param name="param_error" type="float" value="-1.0" label="Filtering by deviation to theoretical mass (disabled for negative values)." help="(-error)"/>
+<remove value="'"/>
-<param name="param_unit" type="select" optional="True" value="ppm" label="Absolute or relativ error." help="(-unit)">
+<remove value="&quot;"/>
-<option value="Da">Da</option>
+</valid>
-<option value="ppm">ppm</option>
+</sanitizer>
 </param>
-<param name="param_n_peptide_hits" type="integer" min="0" optional="True" value="0" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n&gt;0)." help="(-n_peptide_hits)"/>
+<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 name="param_n_protein_hits" type="integer" min="0" optional="True" value="0" label="Keep only the 'n' highest scoring protein hits (for n&gt;0)." help="(-n_protein_hits)"/>
+<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 name="param_strict" type="boolean" truevalue="-best:strict true" falsevalue="-best:strict false" checked="false" optional="True" label="Keep only the highest scoring peptide hit.#br#Similar to n_peptide_hits=1, but if there are two or more highest scoring hits, none are kept." help="(-strict)"/>
+<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"/>
-<expand macro="advanced_options">
+<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 name="param_n_to_m_peptide_hits" type="text" size="20" value=":" label="peptide hit rank range to extracts" help="(-n_to_m_peptide_hits)"/>
+<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"/>
-</expand>
+<param format="fasta" help="(-proteins) &lt;br&gt;All peptides that are not a substring of a sequence in this file are removed &lt;br&gt;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"/>
-</inputs>
+<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"/>
-<outputs>
+<repeat min="0" name="rep_param_whitelist_protein_accessions" title="param_whitelist_protein_accessions">
-<data name="param_out" label="output file " format="idXML"/>
+<param help="(-protein_accessions) &lt;br&gt;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">
-</outputs>
+<sanitizer>
-<help>**What it does**
+<valid initial="string.printable">
+<remove value="'"/>
-Filters results from protein or peptide identification engines based on different criteria.
+<remove value="&quot;"/>
+</valid>
+</sanitizer>
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFilter.html
+</param>
+</repeat>
-@REFERENCES@
+<param format="xml" help="(-peptides) Use with blacklist:ignore_modification flag to only compare by sequence. &lt;br&gt;" 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"/>
-</help>
+<param checked="false" falsevalue="" help="(-ignore_modifications) &lt;br&gt;" label="Compare blacklisted peptides by sequence only" name="param_blacklist_ignore_modifications" optional="True" truevalue="-blacklist:ignore_modifications" type="boolean"/>
-</tool>
+<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&gt;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&gt;0)" min="0" name="param_best_n_protein_hits" optional="True" type="integer" value="0"/>
+<param checked="false" falsevalue="" help="(-strict) &lt;br&gt;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="&quot;"/>
+</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>

Mercurial > repos > bgruening > openms

comparison IDFilter.xml @ 4:6ead64a594bd draft default tip