view chapbook_demo/chapbook_demo.xml @ 149:3b4cd4e35b3a draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 743573b7be16eb3a159ec0affb43ea370cc190f6-dirty

<tool id="CHAP_chapbook_demo" name="CHAPbook" version="@TOOL_VERSION@+galaxy1" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
  <macros>
    <import>../macros.xml</import>
  </macros>
  <requirements>
    <expand macro="chap-requirement" />
    <requirement type="package" version="1.0.1">nexusformat</requirement>
    <requirement type="package" version="2023.3.0">pyfai</requirement>
    <requirement type="package" version="1.10.7">pydantic</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
      pip --exists-action i install certif-pyspec==1.5.3 &&
      cd '$indir' &&
      CHAP --config '$config'
]]></command>
  <environment_variables>
    <environment_variable name="PYTHONPATH">/home/chess_chapaas/chess/chap/</environment_variable>
  </environment_variables>
  <inputs>
      <param type="data" name="config" format="yaml" label="Pipeline Configuration File" />
      <param type="text" name="indir" label="Input Directory" />
  </inputs>
  <outputs>
      <!-- <data name="data" format="nex" label="Reduced data"/> -->
      <!-- <data name="plot" format="png" label="Plot"/> -->
      <collection name="pipeline_output" type="list" label="Pipeline Output">
	<discover_datasets directory="outputs" recurse="true" visible="true"/>
      </collection>
  </outputs>
  <tests>
      <test>
          <param name="config" value="config.yaml"/>
	  <param name="indir" value="/tmp/"/>
      </test>
  </tests>
  <help><![CDATA[
      CHESS Analysis Pipeline (CHAP):

      To run it on command line you'll use:
      CHAP --config CONFIG

      To run it within galaxy you'll only need to upload your
      required configuration pipeline and necessary data.
  ]]></help>
  <citations>
    <expand macro="chap-citation" />
  </citations>
</tool>