Mercurial > repos > galaxyp > openms_psmfeatureextractor
diff PSMFeatureExtractor.xml @ 4:8d4b175e06b5 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
---|---|
date | Thu, 03 Sep 2020 16:20:56 +0000 |
parents | 54ff34feb43d |
children | 151e4b119c70 |
line wrap: on
line diff
--- a/PSMFeatureExtractor.xml Fri May 17 10:14:42 2019 -0400 +++ b/PSMFeatureExtractor.xml Thu Sep 03 16:20:56 2020 +0000 @@ -1,89 +1,89 @@ <?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: [Utilities]--> -<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="2.3.0"> +<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Computes extra features for each input PSM.</description> <macros> <token name="@EXECUTABLE@">PSMFeatureExtractor</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[PSMFeatureExtractor + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re +## Preprocessing +mkdir in && +${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } +mkdir out && + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd -in - #for token in $param_in: - $token - #end for -#if $param_out: - -out $param_out -#end if +${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} +-out +'out/output.${out_type}' -#if $rep_param_extra: --extra - #for token in $rep_param_extra: - #if " " in str(token): - "$token.param_extra" - #else - $token.param_extra - #end if - #end for -#end if -#if $param_multiple_search_engines: - -multiple_search_engines -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_skip_db_check: - -skip_db_check -#end if - #if $adv_opts.param_concat: - -concat -#end if - #if $adv_opts.param_impute: - -impute -#end if - #if $adv_opts.param_limit_imputation: - -limit_imputation -#end if - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +## Postprocessing +&& mv 'out/output.${out_type}' '$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="mzid,idxml" multiple="true" optional="False" size="30" label="Input file(s)" help="(-in) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/> + <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help=""> + <option value="idXML">idxml</option> + <option value="mzid">mzid</option> + <expand macro="list_string_san"/> + </param> + <param name="extra" argument="-extra" type="text" optional="true" value="" label="List of the MetaData parameters to be included in a feature set for precolato" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val"/> + <expand macro="list_string_san"/> </param> - <repeat name="rep_param_extra" min="0" title="param_extra"> - <param name="param_extra" type="text" size="30" label="List of the MetaData parameters to be included in a feature set for precolato" help="(-extra) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="multiple_search_engines" argument="-multiple_search_engines" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Combine PSMs from different search engines by merging on scan level" help=""/> + <expand macro="adv_opts_macro"> + <param name="skip_db_check" argument="-skip_db_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Manual override to skip the check if same settings for multiple search engines were applied" help="Only valid together with -multiple_search_engines flag"/> + <param name="concat" argument="-concat" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="Only valid together with -multiple_search_engines flag"/> + <param name="impute" argument="-impute" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="Only valid together with -multiple_search_engines flag"/> + <param name="limit_imputation" argument="-limit_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="Only valid together with -multiple_search_engines flag"/> + <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> - </repeat> - <param name="param_multiple_search_engines" display="radio" type="boolean" truevalue="-multiple_search_engines" falsevalue="" checked="false" optional="True" label="Combine PSMs from different search engines by merging on scan level" help="(-multiple_search_engines) "/> - <expand macro="advanced_options"> - <param name="param_skip_db_check" display="radio" type="boolean" truevalue="-skip_db_check" falsevalue="" checked="false" optional="True" label="Manual override to skip the check if same settings for multiple search engines were applied" help="(-skip_db_check) Only valid together with -multiple_search_engines flag"/> - <param name="param_concat" display="radio" type="boolean" truevalue="-concat" falsevalue="" checked="false" optional="True" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="(-concat) Only valid together with -multiple_search_engines flag"/> - <param name="param_impute" display="radio" type="boolean" truevalue="-impute" falsevalue="" checked="false" optional="True" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="(-impute) Only valid together with -multiple_search_engines flag"/> - <param name="param_limit_imputation" display="radio" type="boolean" truevalue="-limit_imputation" falsevalue="" checked="false" optional="True" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="(-limit_imputation) Only valid together with -multiple_search_engines flag"/> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> </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> </inputs> <outputs> - <data name="param_out" metadata_source="param_in" format="input"/> + <data name="out" label="${tool.name} on ${on_string}: out"> + <change_format> + <when input="out_type" value="idXML" format="idxml"/> + <when input="out_type" value="mzid" format="mzid"/> + </change_format> + </data> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Computes extra features for each input PSM. + <tests> + <expand macro="autotest_PSMFeatureExtractor"/> + <expand macro="manutest_PSMFeatureExtractor"/> + </tests> + <help><![CDATA[Computes extra features for each input PSM. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_PSMFeatureExtractor.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_PSMFeatureExtractor.html]]></help> + <expand macro="references"/> </tool>