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Merge pull request #59 from keara-soloway/31-cicd-for-galaxy-tools
Unify galaxy tool versions, dependencies on the chessanalysispipeline package, and citations of the same though a new macros.xml file. Add a github action to update the testtoolshed repo whenever a new version of chessanalysispipeline is created.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| name: galaxy-tools | ||
|
|
||
| on: | ||
| push: | ||
| tags: | ||
| - v*.*.* | ||
|
|
||
| jobs: | ||
| update-toolshed-repo: | ||
| runs-on: ubuntu-20.04 | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: '3.9' | ||
| - name: Install planemo | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install planemo | ||
| - name: Update tool version macro with CHAP version (tag) name | ||
| run: | | ||
| sed -i "s/PACKAGE_VERSION/${{ github.ref_name }}/" galaxy-tools/macros.xml | ||
| - name: Update toolshed | ||
| run: | | ||
| planemo shed_update --shed_target testtoolshed --shed_key ${{secrets.XIMGCHESS_TESTTOOLSHED_KEY}}$ galaxy-tools |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,42 +1,37 @@ | ||
| <tool id="CHAP_test" name="CHESS Analysis Pipeline" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05"> | ||
| <requirements> | ||
| <requirement type="package" version="0.0.2">ChessAnalysisPipeline</requirement> | ||
| </requirements> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| cp '$input' data.csv && | ||
| CHAP --config '$config' && | ||
| ]]></command> | ||
| <inputs> | ||
| <param type="data" name="config" format="yaml" /> | ||
| <param type="data" name="input" format="csv" /> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format="json" /> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="config" value="config.yaml"/> | ||
| <param name="input" value="data.csv"/> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| CHESS Analysis Pipeline (CHAP): | ||
| <tool id="CHAP_test" name="CHESS Analysis Pipeline" 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" /> | ||
| </requirements> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| cp '$input' data.csv && | ||
| CHAP --config '$config' && | ||
| ]]></command> | ||
| <inputs> | ||
| <param type="data" name="config" format="yaml" /> | ||
| <param type="data" name="input" format="csv" /> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format="json" /> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="config" value="config.yaml"/> | ||
| <param name="input" value="data.csv"/> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| CHESS Analysis Pipeline (CHAP): | ||
| To run it on command line you'll use: | ||
| CHAP --config CONFIG | ||
| 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> | ||
| <citation type="bibtex"> | ||
| @misc{githubChessAnalysisPipeline, | ||
| author = {LastTODO, FirstTODO}, | ||
| year = {TODO}, | ||
| title = {ChessAnalysisPipeline}, | ||
| publisher = {GitHub}, | ||
| journal = {GitHub repository}, | ||
| url = {https://github.com/CHESSComputing/ChessAnalysisPipeline}, | ||
| }</citation> | ||
| </citations> | ||
| 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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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,12 @@ | ||
| <macros> | ||
| <token name="@TOOL_VERSION@">PACKAGE_VERSION</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <token name="@PROFILE@">21.09</token> | ||
| <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token> | ||
| <xml name="chap-requirement"> | ||
| <requirement type="package" version="@TOOL_VERSION@">chessanalysispipeline</requirement> | ||
| </xml> | ||
| <xml name="chap-citation"> | ||
| <citation type="doi">10.5281/zenodo.7963532</citation> | ||
| </xml> | ||
| </macros> |
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| # Nota: C-Order, 1 refers to the Y axis, 2 to the X axis | ||
| # Calibration done at Wed May 24 10:05:27 2023 | ||
| poni_version: 2 | ||
| Detector: Pilatus300k | ||
| Detector_config: {} | ||
| Distance: 1 | ||
| Poni1: 0 | ||
| Poni2: 0 | ||
| Rot1: 0 | ||
| Rot2: 0 | ||
| Rot3: 0 | ||
| Wavelength: 1.54e-10 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,15 +1,14 @@ | ||
| tool_type: integration | ||
| title: saxs_azimuthal | ||
| title: reduced_data | ||
| integration_type: azimuthal | ||
| detectors: | ||
| - prefix: PIL5 | ||
| poni_file: PIL5.poni | ||
| mask_file: PIL5.tif | ||
| radial_units: q_A^-1 | ||
| radial_min: 0.0 | ||
| radial_max: 0.21821 | ||
| - prefix: det | ||
| poni_file: det.poni | ||
| radial_units: q_nm^-1 | ||
| radial_min: 0.01372382 | ||
| radial_max: 5.47580553 | ||
| radial_npt: 200 | ||
| azimuthal_units: chi_deg | ||
| azimuthal_min: -180.0 | ||
| azimuthal_max: 180.0 | ||
| azimuthal_npt: 180 | ||
| azimuthal_npt: 180 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,48 +1,43 @@ | ||
| <tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05"> | ||
| <requirements> | ||
| <requirement type="package" version="0.0.8">chessanalysispipeline</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 '$__tool_directory__/pipeline.yaml' | ||
| ]]></command> | ||
| <inputs> | ||
| <param type="data" name="mapconfig" format="yaml" /> | ||
| <param type="data" name="integrationconfig" format="yaml" /> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="reduceddata" label="Map of reduced data" format="nex" from_work_dir="map_reduceddata.nxs"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="mapconfig" value="map.yaml"/> | ||
| <param name="integrationconfig" value="integration.yaml"/> | ||
| <output name="reduceddata" value="map_reduceddata.nxs"/> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| usage: PROG [-h] [--config CONFIG] [--verbose] | ||
| <tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@"> | ||
| <macros> | ||
| <import>../macros.xml</import> | ||
| </macros> | ||
| <requirements> | ||
| <expand macro="chap-requirement" /> | ||
| <requirement type="package" version="1.0.1">nexusformat</requirement> | ||
| <requirement type="package" version="2023.3.0">pyfai</requirement> | ||
| <requirement type="package" version="1.10.7">pydantic</requirement> | ||
| </requirements> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| pip --exists-action i install certif-pyspec==1.5.3 && | ||
| cp '$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> | ||
| <citation type="bibtex"> | ||
| @misc{githubChessAnalysisPipeline, | ||
| author = {LastTODO, FirstTODO}, | ||
| year = {TODO}, | ||
| title = {CHAPSAXSWAXSdemo}, | ||
| publisher = {GitHub}, | ||
| journal = {GitHub repository}, | ||
| url = {https://github.com/CHESSComputing/ChessAnalysisPipeline}, | ||
| }</citation> | ||
| </citations> | ||
| ]]></help> | ||
| <citations> | ||
| <expand macro="chap-citation" /> | ||
| </citations> | ||
| </tool> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| #F test_scans | ||
| #E 1684937343 | ||
| #O0 mtr_0 | ||
| #o0 mtr_0 | ||
| #S 1 ascan mtr_1 -1 1 2 1 | ||
| #P0 -1 | ||
| #L mtr_1 counter_0 | ||
| -1 0.5970827916509526 | ||
| 0 0.8235129241022665 | ||
| 1 0.5112369186482792 | ||
| #S 2 ascan mtr_1 -1 1 2 1 | ||
| #P0 0 | ||
| #L mtr_1 counter_0 | ||
| -1 0.5993819559229079 | ||
| 0 0.7377995537968701 | ||
| 1 0.1865718135324972 | ||
| #S 3 ascan mtr_1 -1 1 2 1 | ||
| #P0 1 | ||
| #L mtr_1 counter_0 | ||
| -1 0.9943311654787657 | ||
| 0 0.07937636730740139 | ||
| 1 0.021956904524402576 |
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