<?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="@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="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
#if $in:
  mkdir in &&
  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
#end if
#if $run:
  mkdir run &&
  ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
#end if
#if $plot:
  mkdir plot &&
  ln -s '$plot' 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' &&
#end if
#if $table:
  mkdir table &&
  ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.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
#if $in:
  -in
  'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
#end if
#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
#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="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="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="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>
  </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>
    <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 http://www.openms.de/documentation/UTILS_QCEmbedder.html]]></help>
  <expand macro="references"/>
</tool>