view chapbook_demo/chapbook_demo.xml @ 166:f554351c0a06 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit c860fa7080cf5e8038672a876975bc7f9ca26d59

<tool id="CHAP_chapbook_demo" name="CHAPbook" version="@TOOL_VERSION@+galaxy13" 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[
      ## certif-pyspec is not available over any conda channels, so
      ## pip install the package the first time this tool is run
      pip --exists-action i install certif-pyspec==1.5.3 &&

      ## Create symlinks in the tool directory to all items in the
      ## input directory provided by the user
      #import os.path
      #set $norm_indir = os.path.normpath(str($indir))
      ln -s $norm_indir/* . &&

      ## Run the pipeline provided
      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" from_work_dir="data.nex"/>
      <data name="plot" format="png" label="Plot" from_work_dir="plot.png"/>
  </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>