<!--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: []-->
<tool id="QCShrinker" name="QCShrinker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <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>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
#if $run:
  mkdir run &&
  cp '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
#end if
mkdir out &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
#if $run:
  -run
  'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)'
#end if
-out
'out/output.${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 argument="-in" type="data" format="qcml" label="Input qcml file" help=" select qcml data sets(s)"/>
    <param 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" name="qp_accessions"/>
      <expand macro="list_string_san" name="qp_accessions"/>
    </param>
    <param 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" name="name"/>
    </param>
    <param 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 argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <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>
  <tests>
    <test expect_num_outputs="1">
      <!-- just using an output of QCCalculator as input  -->
      <param name="adv_opts|test" value="true"/>
      <param name="in" ftype="qcml" value="QCCalculator1.qcML"/>
      <output name="out" ftype="qcml" value="QCShrinker.qcML"/>
    </test>
  </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://openms.de/doxygen/release/3.1.0/html/TOPP_QCShrinker.html]]></help>
  <expand macro="references"/>
</tool>