Mercurial > repos > galaxyp > openms_idsplitter
diff IDSplitter.xml @ 9:629b818f162c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 12:44:13 +0000 |
parents | 0a61c5337abf |
children | de2d6f629cea |
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--- a/IDSplitter.xml Fri May 17 09:19:59 2019 -0400 +++ b/IDSplitter.xml Wed Sep 09 12:44:13 2020 +0000 @@ -1,44 +1,99 @@ <?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="IDSplitter" name="IDSplitter" version="2.3.0"> +<tool id="IDSplitter" name="IDSplitter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Splits protein/peptide identifications off of annotated data files</description> <macros> <token name="@EXECUTABLE@">IDSplitter</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[IDSplitter + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $param_in: - -in $param_in +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir out && +#end if +#if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir id_out && #end if -#if $param_out: - -out $param_out + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -out + 'out/output.${in.ext}' #end if -#if $param_id_out: - -id_out $param_id_out +#if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -id_out + 'id_out/output.${gxy2omsext("idxml")}' +#end if +#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 + | tee '$stdout' #end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force + +## Postprocessing +#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'out/output.${in.ext}' '$out' +#end if +#if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'id_out/output.${gxy2omsext("idxml")}' '$id_out' #end if -#end if -]]></command> +#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="mzml,featurexml,consensusxml" optional="False" label="Input file (data annotated with identifications)" help="(-in) "/> - <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) "/> + <param name="in" argument="-in" type="data" format="consensusxml,featurexml,mzml" optional="false" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml,mzml data sets(s)"/> + <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="false"> + <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option> + <option value="id_out_FLAG">id_out (Enables the test mode (needed for internal use only))</option> + <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="param_id_out" format="idxml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"> + <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="id_out" label="${tool.name} on ${on_string}: id_out" format="idxml"> + <filter>OPTIONAL_OUTPUTS is not None and "id_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> + <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> + <filter>OPTIONAL_OUTPUTS is None</filter> + </data> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Splits protein/peptide identifications off of annotated data files + <tests> + <expand macro="autotest_IDSplitter"/> + <expand macro="manutest_IDSplitter"/> + </tests> + <help><![CDATA[Splits protein/peptide identifications off of annotated data files -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_IDSplitter.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_IDSplitter.html]]></help> + <expand macro="references"/> </tool>