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add: galaxy tool for user processor demo
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keara-soloway committed Jun 26, 2023
1 parent 819e366 commit 743573b
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45 changes: 45 additions & 0 deletions galaxy-tools/chapbook_demo/chapbook_demo.xml
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<tool id="CHAP_chapbook_demo" name="CHAPbook" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 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"/>
</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>

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