Mercurial > repos > galaxyp > openms_qcshrinker
diff QCShrinker.xml @ 9:ccfc3e189087 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 20:13:29 +0000 |
parents | 52720a19f8f1 |
children | 910f1fdf039a |
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--- a/QCShrinker.xml Fri May 17 09:39:53 2019 -0400 +++ b/QCShrinker.xml Wed Sep 09 20:13:29 2020 +0000 @@ -1,76 +1,86 @@ <?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="QCShrinker" name="QCShrinker" version="2.3.0"> +<tool id="QCShrinker" name="QCShrinker" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</description> <macros> <token name="@EXECUTABLE@">QCShrinker</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> - <expand macro="stdio"/> <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[QCShrinker - -#if $param_in: - -in $param_in -#end if + <expand macro="stdio"/> + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $rep_param_qp_accessions: --qp_accessions - #for token in $rep_param_qp_accessions: - #if " " in str(token): - "$token.param_qp_accessions" - #else - $token.param_qp_accessions - #end if - #end for +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +#if $run: + mkdir run && + ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' && #end if -#if $param_name: - -name "$param_name" -#end if -#if $param_run: - -run $param_run -#end if -#if $param_out: - -out $param_out +mkdir out && + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +#if $run: + -run + 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' #end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +-out +'out/output.${gxy2omsext("qcml")}' + +## Postprocessing +&& mv 'out/output.${gxy2omsext("qcml")}' '$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="qcml" optional="False" label="Input qcml file" help="(-in) "/> - <repeat name="rep_param_qp_accessions" min="0" title="param_qp_accessions"> - <param name="param_qp_accessions" type="text" size="30" label="A list of cv accessions that should be removed" help="(-qp_accessions) If empty, the usual suspects will be removed!"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="in" argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/> + <param name="qp_accessions" argument="-qp_accessions" type="text" optional="true" value="" label="A list of cv accessions that should be removed" help="If empty, the usual suspects will be removed! (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> + <param name="name" argument="-name" type="text" optional="true" value="" label="The name of the target run or set that contains the requested quality paramete" help=""> + <expand macro="list_string_san"/> + </param> + <param name="run" argument="-run" type="data" format="mzml" optional="true" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="This overrides the name parameter! select 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> - </repeat> - <param name="param_name" type="text" size="30" label="The name of the target run or set that contains the requested quality paramete" help="(-name) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + </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_run" type="data" format="mzml" optional="True" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="(-run) This overrides the name parameter!"/> - <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" format="qcml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report. + <tests> + <expand macro="autotest_QCShrinker"/> + <expand macro="manutest_QCShrinker"/> + </tests> + <help><![CDATA[This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_QCShrinker.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_QCShrinker.html]]></help> + <expand macro="references"/> </tool>