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add: galaxy tool for user processor demo
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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> |