view saqc_executor.xml @ 0:99e2019c318c draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe

<tool name="SaQC executor" id="saqc_executor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
  <description>quality control for time series</description>
  <creator>
    <organization name="Helmholtz Centre for Environmental Research - UFZ, Research Data Management"
                  url ="https://www.ufz.de/index.php?en=45348"/>
  </creator>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command><![CDATA[python -c 'import saqc; print(saqc.__version__)']]></version_command>
   <command detect_errors="exit_code"><![CDATA[
  ln -s '$config' config.csv &&
  #for $i, $d in enumerate($data)
      ln -s '$d' '${i}.csv' &&
  #end for
  saqc -c config.csv
  #for $i, $d in enumerate($data)
      -d '${i}.csv'
  #end for
  -o output.csv
  ]]></command>
  <inputs>
    <param label="Input Table(s)"
           argument="--data"
           type="data"
           format="csv"
           multiple="true"
           optional="false"
    />
    <param label="Configuration"
           argument="--config"
           type="data"
           format="txt"
           optional="false"/>
  </inputs>
  <outputs>
      <data name="output"
            format="csv"
            from_work_dir="output.csv"
            hidden="false"/>
  </outputs>
  <tests>
    <test>
      <!-- https://rdm-software.pages.ufz.de/saqc/cookbooks/MultivariateFlagging.html -->
      <param name="data" value="data.csv,maint.csv" ftype="csv"/>
      <param name="config" value="config.txt" ftype="txt"/>
      <output name="output" value="out.csv" ftype="csv"/>
    </test>
  </tests>
  <help><![CDATA[
  This tool runs the SaQC quality control pipeline specified by a config file on the input data.
  Just upload your data and a config file, and the tool will run the SaQC pipeline on the data.
]]></help>
  <expand macro="citations"/>
</tool>