Mercurial > repos > ximgchess > chap_test_20230411
changeset 148:cef6aa4b716a draft
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 743573b7be16eb3a159ec0affb43ea370cc190f6-dirty
| author | ximgchess |
|---|---|
| date | Mon, 26 Jun 2023 12:56:52 +0000 |
| parents | 24113e913212 |
| children | 3b4cd4e35b3a |
| files | chapbook_demo/chapbook_demo.xml macros.xml |
| diffstat | 2 files changed, 46 insertions(+), 1 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chapbook_demo/chapbook_demo.xml Mon Jun 26 12:56:52 2023 +0000 @@ -0,0 +1,45 @@ +<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>
--- a/macros.xml Mon Jun 26 12:54:36 2023 +0000 +++ b/macros.xml Mon Jun 26 12:56:52 2023 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">v0.0.9</token> + <token name="@TOOL_VERSION@">0.0.9</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.09</token> <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token>