Mercurial > repos > galaxyp > openms_consensusid
diff ConsensusID.xml @ 13:fdc984e79f40 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
| author | galaxyp |
|---|---|
| date | Thu, 27 Aug 2020 19:43:01 -0400 |
| parents | 368221d85573 |
| children | feebe2054e40 |
line wrap: on
line diff
--- a/ConsensusID.xml Fri May 17 10:09:43 2019 -0400 +++ b/ConsensusID.xml Thu Aug 27 19:43:01 2020 -0400 @@ -1,100 +1,98 @@ <?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 CTDConverter.--> <!--Proposed Tool Section: [ID Processing]--> -<tool id="ConsensusID" name="ConsensusID" version="2.3.0"> +<tool id="ConsensusID" name="ConsensusID" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Computes a consensus of peptide identifications of several identification engines.</description> <macros> <token name="@EXECUTABLE@">ConsensusID</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[ConsensusID + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re + +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +mkdir out && + +## Main program call -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_rt_delta: - -rt_delta $param_rt_delta -#end if -#if $param_mz_delta: - -mz_delta $param_mz_delta -#end if -#if $param_algorithm: - -algorithm - #if " " in str($param_algorithm): - "$param_algorithm" - #else - $param_algorithm - #end if -#end if -#if $param_filter_considered_hits: - -filter:considered_hits $param_filter_considered_hits -#end if -#if $param_filter_min_support: - -filter:min_support $param_filter_min_support -#end if -#if $param_filter_count_empty: - -filter:count_empty -#end if -#if $param_PEPIons_mass_tolerance: - -PEPIons:mass_tolerance $param_PEPIons_mass_tolerance -#end if -#if $param_PEPIons_min_shared: - -PEPIons:min_shared $param_PEPIons_min_shared -#end if -#if $param_PEPMatrix_matrix: - -PEPMatrix:matrix - #if " " in str($param_PEPMatrix_matrix): - "$param_PEPMatrix_matrix" - #else - $param_PEPMatrix_matrix - #end if -#end if -#if $param_PEPMatrix_penalty: - -PEPMatrix:penalty $param_PEPMatrix_penalty -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +-out +'out/output.${in.ext}' + +## Postprocessing +&& mv 'out/output.${in.ext}' '$out' +#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS + && mv '@EXECUTABLE@.ctd' '$ctd_out' +#end if]]></command> + <configfiles> + <inputs name="args_json" data_style="paths"/> + <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <param name="param_in" type="data" format="idxml,featurexml,consensusxml" optional="False" label="input file" help="(-in) "/> - <param name="param_rt_delta" type="float" min="0.0" optional="True" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help="(-rt_delta) "/> - <param name="param_mz_delta" type="float" min="0.0" optional="True" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help="(-mz_delta) "/> - <param name="param_algorithm" type="select" optional="False" value="PEPMatrix" label="Algorithm used for consensus scoring" help="(-algorithm) <br>* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores. <br>* PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores. <br>* best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs. <br>* worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs. <br>* average: For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs. <br>* ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types"> + <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="input file" help=" select consensusxml,featurexml,idxml data sets(s)"/> + <param name="rt_delta" argument="-rt_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help=""/> + <param name="mz_delta" argument="-mz_delta" type="float" optional="true" min="0.0" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help=""/> + <param name="algorithm" argument="-algorithm" type="select" optional="false" label="Algorithm used for consensus scoring" help="* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores.. * PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores.. * best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs.. * worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs.. * average: For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs.. * ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types"> <option value="PEPMatrix" selected="true">PEPMatrix</option> <option value="PEPIons">PEPIons</option> <option value="best">best</option> <option value="worst">worst</option> <option value="average">average</option> <option value="ranks">ranks</option> + <expand macro="list_string_san"/> </param> - <param name="param_filter_considered_hits" type="integer" min="0" optional="True" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help="(-considered_hits) "/> - <param name="param_filter_min_support" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help="(-min_support) "/> - <param name="param_filter_count_empty" display="radio" type="boolean" truevalue="-filter:count_empty" falsevalue="" checked="false" optional="True" label="Count empty ID runs (i.e" help="(-count_empty) those containing no peptide hit for the current spectrum) when calculating 'min_support'?"/> - <param name="param_PEPIons_mass_tolerance" type="float" min="0.0" optional="True" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help="(-mass_tolerance) "/> - <param name="param_PEPIons_min_shared" type="integer" min="1" optional="True" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help="(-min_shared) "/> - <param name="param_PEPMatrix_matrix" display="radio" type="select" optional="False" value="identity" label="Substitution matrix to use for alignment-based similarity scoring" help="(-matrix) "> - <option value="identity" selected="true">identity</option> - <option value="PAM30MS">PAM30MS</option> + <section name="filter" title="Options for filtering peptide hits" help="" expanded="false"> + <param name="considered_hits" argument="-filter:considered_hits" type="integer" optional="true" min="0" value="0" label="The number of top hits in each ID run that are considered for consensus scoring ('0' for all hits)" help=""/> + <param name="min_support" argument="-filter:min_support" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="For each peptide hit from an ID run, the fraction of other ID runs that must support that hit (otherwise it is removed)" help=""/> + <param name="count_empty" argument="-filter:count_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Count empty ID runs" help="(i.e. those containing no peptide hit for the current spectrum) when calculating 'min_support'?"/> + </section> + <section name="PEPIons" title="PEPIons algorithm parameters" help="" expanded="false"> + <param name="mass_tolerance" argument="-PEPIons:mass_tolerance" type="float" optional="true" min="0.0" value="0.5" label="Maximum difference between fragment masses (in Da) for fragments to be considered 'shared' between peptides" help=""/> + <param name="min_shared" argument="-PEPIons:min_shared" type="integer" optional="true" min="1" value="2" label="The minimal number of 'shared' fragments (between two suggested peptides) that is necessary to evaluate the similarity based on shared peak count (SPC)" help=""/> + </section> + <section name="PEPMatrix" title="PEPMatrix algorithm parameters" help="" expanded="false"> + <param name="matrix" argument="-PEPMatrix:matrix" display="radio" type="select" optional="false" label="Substitution matrix to use for alignment-based similarity scoring" help=""> + <option value="identity" selected="true">identity</option> + <option value="PAM30MS">PAM30MS</option> + <expand macro="list_string_san"/> + </param> + <param name="penalty" argument="-PEPMatrix:penalty" type="integer" optional="true" min="1" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help=""/> + </section> + <expand macro="adv_opts_macro"> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> + </param> + </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> - <param name="param_PEPMatrix_penalty" type="integer" min="1" optional="True" value="5" label="Alignment gap penalty (the same value is used for gap opening and extension)" help="(-penalty) "/> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> - </expand> </inputs> <outputs> - <data name="param_out" metadata_source="param_in" format="input"/> + <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Computes a consensus of peptide identifications of several identification engines. + <tests> + <expand macro="autotest_ConsensusID"/> + <expand macro="manutest_ConsensusID"/> + </tests> + <help><![CDATA[Computes a consensus of peptide identifications of several identification engines. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ConsensusID.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_ConsensusID.html]]></help> + <expand macro="references"/> </tool>