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changeset 19:4b553f7fb7fb draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 2e1e853d16782d778b15f82fb5760874382b36e9
author kls286
date Tue, 11 Apr 2023 11:10:48 +0000
parents f7133218d7c3
children fc1b08c6fa10
files chap.xml integration.yaml map.yaml pipeline.yaml reduce.xml saxswaxs-config/integration.yaml saxswaxs-config/map.yaml saxswaxs-config/pipeline.yaml saxswaxs.xml
diffstat 9 files changed, 121 insertions(+), 164 deletions(-) [+]
line wrap: on
line diff
--- a/chap.xml	Tue Apr 04 16:57:20 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-<tool id="chap" 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="csv" from_work_dir="data.out"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="config" value="config.yaml"/>
-            <param name="input" value="data.csv"/>
-            <output name="output" value="data.out"/>
-        </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 = {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/integration.yaml	Tue Apr 11 11:10:48 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/map.yaml	Tue Apr 11 11:10:48 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/pipeline.yaml	Tue Apr 11 11:10:48 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/reduce.xml	Tue Apr 11 11:10:48 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>
--- a/saxswaxs-config/integration.yaml	Tue Apr 04 16:57:20 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-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
--- a/saxswaxs-config/map.yaml	Tue Apr 04 16:57:20 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-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
--- a/saxswaxs-config/pipeline.yaml	Tue Apr 04 16:57:20 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-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
--- a/saxswaxs.xml	Tue Apr 04 16:57:20 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-<tool id="saxswaxs-test" name="SAXSWAXS Demo Pipeline" 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[
-        cp '$mapconfig' map.yaml &&
-	cp '$integrationconfig' integration.yaml &&
-	cp '$__tool_directory__/saxswaxs-config/pipeline.yaml' saxswaxs-pipeline.yaml &&
-	CHAP --config saxswaxs-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="saxswaxs-config/map.yaml"/>
-            <param name="integrationconfig" value="saxswaxs-config/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>