Mercurial > repos > ximgchess > chap_test_20230411
changeset 168:7883df4af8ab draft default tip
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 509f8f9b035d9dc3f4878cea2d14769819fe2349-dirty
author | ximgchess |
---|---|
date | Wed, 23 Aug 2023 18:33:28 +0000 |
parents | 50fb82e1213a |
children | |
files | chapbook_demo/chapbook_demo.xml macros.xml tomo/tomo_macros.xml |
diffstat | 3 files changed, 5 insertions(+), 15 deletions(-) [+] |
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--- a/chapbook_demo/chapbook_demo.xml Wed Jul 05 13:37:14 2023 +0000 +++ b/chapbook_demo/chapbook_demo.xml Wed Aug 23 18:33:28 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="CHAP_chapbook_demo" name="CHAPbook" version="@TOOL_VERSION@+galaxy13" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@"> +<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> @@ -9,17 +9,8 @@ <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 $norm_indir/* . && - - ## Run the pipeline provided + cd '$indir' && CHAP --config '$config' ]]></command> <environment_variables> @@ -30,8 +21,8 @@ <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"/> + <data name="data" format="nex" label="Reduced data"/> + <data name="plot" format="png" label="Plot"/> </outputs> <tests> <test>
--- a/macros.xml Wed Jul 05 13:37:14 2023 +0000 +++ b/macros.xml Wed Aug 23 18:33:28 2023 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">0.0.10</token> + <token name="@TOOL_VERSION@">0.0.11</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.09</token> <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token>
--- a/tomo/tomo_macros.xml Wed Jul 05 13:37:14 2023 +0000 +++ b/tomo/tomo_macros.xml Wed Aug 23 18:33:28 2023 +0000 @@ -2,7 +2,6 @@ <xml name="requirements"> <requirements> <expand macro="chap-requirement" /> - <requirement type="package" version="0.0.8">chessanalysispipeline</requirement> <requirement type="package" version="1.1.0">lmfit</requirement> <requirement type="package" version="3.7.1">matplotlib</requirement> <requirement type="package" version="1.0.1">nexusformat</requirement>