view saxswaxs/reduce.xml @ 127:d8baf7dafbd8 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit dfe15e79689bca8ddcd843f9cf47eff29f6ee2e4-dirty

<tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
    <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 &&
        cp '$mapconfig' map.yaml &&
	cp '$integrationconfig' integration.yaml &&
	CHAP --config '$__tool_directory__/pipeline.yaml'
    ]]></command>
    <inputs>
        <param type="data" name="mapconfig" format="yaml" />
        <param type="data" name="integrationconfig" format="yaml" />
    </inputs>
    <outputs>
	<data name="reduceddata" label="Map of reduced data" format="nex" from_work_dir="map_reduceddata.nxs"/>
    </outputs>
    <tests>
        <test>
            <param name="mapconfig" value="map.yaml"/>
            <param name="integrationconfig" value="integration.yaml"/>
            <output name="reduceddata" value="map_reduceddata.nxs"/>
        </test>
    </tests>
    <help><![CDATA[
        usage: PROG [-h] [--config CONFIG] [--verbose]

options:
  -h, --help       show this help message and exit
  --config CONFIG  Input configuration file
  --verbose        verbose output

    ]]></help>
    <citations>
        <expand macro="chap-citation" />
    </citations>
</tool>