Mercurial > repos > galaxyp > openms_qcembedder
diff QCEmbedder.xml @ 9:254e748f243a 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 12:47:21 +0000 |
parents | 059c20a50b1d |
children | 2c6f5858e89a |
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--- a/QCEmbedder.xml Fri May 17 09:39:22 2019 -0400 +++ b/QCEmbedder.xml Wed Sep 09 12:47:21 2020 +0000 @@ -1,85 +1,110 @@ <?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="QCEmbedder" name="QCEmbedder" version="2.3.0"> +<tool id="QCEmbedder" name="QCEmbedder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Attaches a table or an image to a given qc parameter.</description> <macros> <token name="@EXECUTABLE@">QCEmbedder</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[QCEmbedder + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $param_in: - -in $param_in +## Preprocessing +#if $in: + mkdir in && + ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #end if -#if $param_qp_att_acc: - -qp_att_acc "$param_qp_att_acc" -#end if -#if $param_cv_acc: - -cv_acc "$param_cv_acc" +#if $run: + mkdir run && + ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' && #end if -#if $param_run: - -run $param_run +#if $plot: + mkdir plot && + ln -s '$plot' 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' && #end if -#if $param_name: - -name "$param_name" -#end if -#if $param_plot: - -plot $param_plot +#if $table: + mkdir table && + ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' && #end if -#if $param_table: - -table $param_table +mkdir out && + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +#if $in: + -in + 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' #end if -#if $param_out: - -out $param_out -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force +#if $run: + -run + 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' #end if +#if $plot: + -plot + 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' #end if -]]></command> +#if $table: + -table + 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' +#end if +-out +'out/output.${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="True" label="Input qcml file" help="(-in) "/> - <param name="param_qp_att_acc" type="text" size="30" label="Defines the qp cv accession of the qp to which the table/image is attached" help="(-qp_att_acc) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="in" argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/> + <param name="qp_att_acc" argument="-qp_att_acc" type="text" optional="true" value="" label="Defines the qp cv accession of the qp to which the table/image is attached" help=""> + <expand macro="list_string_san"/> </param> - <param name="param_cv_acc" type="text" size="30" label="Defines the cv accession of the attachment" help="(-cv_acc) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="cv_acc" argument="-cv_acc" type="text" optional="false" value="" label="Defines the cv accession of the attachment" help=""> + <expand macro="list_string_san"/> + </param> + <param name="run" argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/> + <param name="name" argument="-name" type="text" optional="true" value="" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help=""> + <expand macro="list_string_san"/> </param> - <param name="param_run" type="data" format="mzml" optional="True" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="(-run) The file is only used to extract the run name from the file name"/> - <param name="param_name" type="text" size="30" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help="(-name) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> + <param name="plot" argument="-plot" type="data" format="png" optional="true" label="If a plot image is to be attached to a qp, this has to be specified here" help=" select png data sets(s)"/> + <param name="table" argument="-table" type="data" format="csv" optional="true" label="If a table is to be attached to a qp, this has to be specified here" help=" select csv 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="true"> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> - <param name="param_plot" type="data" format="PNG" optional="True" label="If a plot image is to be attached to a qp, this has to be specified here" help="(-plot) "/> - <param name="param_table" type="data" format="tabular" optional="True" label="If a table is to be attached to a qp, this has to be specified here" help="(-table) "/> - <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>Attaches a table or an image to a given qc parameter. + <tests> + <expand macro="autotest_QCEmbedder"/> + <expand macro="manutest_QCEmbedder"/> + </tests> + <help><![CDATA[Attaches a table or an image to a given qc parameter. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_QCEmbedder.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_QCEmbedder.html]]></help> + <expand macro="references"/> </tool>