view QCExporter.xml @ 10:bd8735ccc6f6 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e9568c650259d95b230d1a243e90f73a19564c2"

<?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="QCExporter" name="QCExporter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Will extract several qp from several run/sets in a tabular format.</description>
  <macros>
    <token name="@EXECUTABLE@">QCExporter</token>
    <import>macros.xml</import>
    <import>macros_autotest.xml</import>
    <import>macros_test.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <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($in.ext)' &&
mkdir mapping &&
ln -s '$mapping' 'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)' &&
mkdir out_csv &&

## 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($in.ext)'
-mapping
'mapping/${re.sub("[^\w\-_]", "_", $mapping.element_identifier)}.$gxy2omsext($mapping.ext)'
-out_csv
'out_csv/output.${gxy2omsext("csv")}'

## Postprocessing
&& mv 'out_csv/output.${gxy2omsext("csv")}' '$out_csv'
#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="in" argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/>
    <param name="names" argument="-names" type="text" optional="true" value="" label="The name of the target runs or sets to be exported from" help="If empty, from all will be exported (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="mapping" argument="-mapping" type="data" format="csv" optional="false" label="The mapping of the exported table's headers to the according qp cvs" help="The first row is considered containing the headers as for the exported the table. The second row is considered the according qp cv accessions of the qp to be exported 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>
  </inputs>
  <outputs>
    <data name="out_csv" label="${tool.name} on ${on_string}: out_csv" format="csv"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <expand macro="autotest_QCExporter"/>
    <expand macro="manutest_QCExporter"/>
  </tests>
  <help><![CDATA[Will extract several qp from several run/sets in a tabular format.


For more information, visit http://www.openms.de/documentation/UTILS_QCExporter.html]]></help>
  <expand macro="references"/>
</tool>