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changeset 0:47d2a1f087d1 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
author ximgchess
date Tue, 11 Apr 2023 14:41:16 +0000
parents
children 84a215623d9e
files chap/chap.xml inference/chapmlaas.xml saxswaxs/ignoreshed.yml saxswaxs/integration.yaml saxswaxs/klspipeline.yaml saxswaxs/map.yaml saxswaxs/pipeline.yaml saxswaxs/reduce.xml
diffstat 8 files changed, 262 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chap/chap.xml	Tue Apr 11 14:41:16 2023 +0000
@@ -0,0 +1,42 @@
+<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):
+
+        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>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/inference/chapmlaas.xml	Tue Apr 11 14:41:16 2023 +0000
@@ -0,0 +1,59 @@
+<tool id="CHAP_inference_demo" name="CHAP MLaaS" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+    <requirements>
+        <requirement type="package" version="2.28.2">requests</requirement>
+        <requirement type="package" version="0.0.2">chessanalysispipeline</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        cp '$input' data.csv &&
+        cp '$image' img.png &&
+        CHAP --config '$config' &&
+        cp preds.json '$output'
+    ]]></command>
+    <inputs>
+        <param type="data" name="config" format="yaml" />
+        <param type="data" name="input" format="csv" />
+        <param type="data" name="image" format="png" />
+    </inputs>
+    <outputs>
+        <data name="output" format="json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="config" value="config.yaml"/>
+            <param name="input" value="data.csv"/>
+            <param name="image" value="img.png"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+CHESS Analysis Pipeline (CHAP) with Machine Learning as a Service (MLaaS)
+
+To run it you need the following:
+1. Working TFaaS server
+2. A pipeline config with TFaaS, e.g.
+
+pipeline:
+  - reader.Reader:
+      filename: data.csv
+  - processor.Processor: {}
+  - reader.BinaryFileReader:
+      filename: img.png
+  - processor.TFaaSImageProcessor:
+      url: "http://localhost:8083"
+      model: mnist
+      verbose: true
+  - writer.Writer:
+      filename: preds.json
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubChessAnalysisPipeline,
+  author = {Kuznetsov, Valentin},
+  year = {2023},
+  title = {ChessAnalysisPipeline},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/CHESSComputing/ChessAnalysisPipeline},
+}</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saxswaxs/ignoreshed.yml	Tue Apr 11 14:41:16 2023 +0000
@@ -0,0 +1,7 @@
+name: chap_test_20230328
+owner: kls286
+description: A generic test pipeline for CHAP
+remote_repository_url: https://github.com/CHESSComputing/ChessAnalysisPipeline
+type: unrestricted
+categories:
+- Structural Materials Analysis
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saxswaxs/integration.yaml	Tue Apr 11 14:41:16 2023 +0000
@@ -0,0 +1,15 @@
+tool_type: integration
+title: saxs_azimuthal
+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
+radial_npt: 200
+azimuthal_units: chi_deg
+azimuthal_min: -180.0
+azimuthal_max: 180.0
+azimuthal_npt: 180
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saxswaxs/klspipeline.yaml	Tue Apr 11 14:41:16 2023 +0000
@@ -0,0 +1,33 @@
+pipeline:
+
+  # Download example data
+  - common.URLReader:
+      url: https://gitlab01.classe.cornell.edu/api/v4/projects/308/repository/files/saxswaxs%2frawdata_test_1d.tar/raw?ref=main
+      headers:
+        PRIVATE-TOKEN: glpat-sH-sniHbynCxUDJBpv5V # your token here
+  - common.URLResponseProcessor
+  - common.ExtractArchiveWriter:
+      filename: .
+
+  # Collect map data
+  - common.YAMLReader:
+      filename: map.yaml
+      schema: MapConfig
+  - common.MapProcessor
+  - common.NexusWriter:
+      filename: map_specdata.nxs
+      force_overwrite: true
+
+  # Integrate map detetcor data
+  - common.MultipleReader:
+      readers:
+        - YAMLReader:
+            filename: map.yaml
+            schema: MapConfig
+        - YAMLReader:
+            filename: integration.yaml
+            schema: IntegrationConfig
+  - common.IntegrateMapProcessor
+  - common.NexusWriter:
+      filename: map_reduceddata.nxs
+      force_overwrite: true
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saxswaxs/map.yaml	Tue Apr 11 14:41:16 2023 +0000
@@ -0,0 +1,23 @@
+title: test_1d
+station: id3b
+experiment_type: SAXSWAXS
+sample:
+  name: sample_14_align
+spec_scans:
+- spec_file: test_1d
+  scan_numbers:
+  - 1
+independent_dimensions:
+- label: samx
+  units: mm
+  data_type: spec_motor
+  name: samx
+presample_intensity:
+  data_type: scan_column
+  name: ic3
+dwell_time_actual:
+  data_type: scan_column
+  name: sec_2
+postsample_intensity:
+  data_type: scan_column
+  name: diode
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saxswaxs/pipeline.yaml	Tue Apr 11 14:41:16 2023 +0000
@@ -0,0 +1,33 @@
+pipeline:
+
+  # Download example data
+  - common.URLReader:
+      url: https://gitlab01.classe.cornell.edu/api/v4/projects/308/repository/files/saxswaxs%2frawdata_test_1d.tar/raw?ref=main
+      headers:
+        PRIVATE-TOKEN: # your token here
+  - common.URLResponseProcessor
+  - common.ExtractArchiveWriter:
+      filename: .
+
+  # Collect map data
+  - common.YAMLReader:
+      filename: map.yaml
+      schema: MapConfig
+  - common.MapProcessor
+  - common.NexusWriter:
+      filename: map_specdata.nxs
+      force_overwrite: true
+
+  # Integrate map detetcor data
+  - common.MultipleReader:
+      readers:
+        - YAMLReader:
+            filename: map.yaml
+            schema: MapConfig
+        - YAMLReader:
+            filename: integration.yaml
+            schema: IntegrationConfig
+  - common.IntegrateMapProcessor
+  - common.NexusWriter:
+      filename: map_reduceddata.nxs
+      force_overwrite: true
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saxswaxs/reduce.xml	Tue Apr 11 14:41:16 2023 +0000
@@ -0,0 +1,50 @@
+<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="0.0.3">chessanalysispipeline</requirement>
+      <requirement type="package" version="2.28.1">requests</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="specdata" label="Map of SPEC data" format="nex" from_work_dir="map_specdata.nxs"/>
+	<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="specdata" value="map_specdata.nxs"/>
+            <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>
+</tool>