Mercurial > repos > ximgchess > chap_test_20230411

changeset 126:ca285a3cc30b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit e77d79bf9a41af058415953e35d20a42e014d90a
author ximgchess
date Tue, 30 May 2023 18:03:00 +0000
parents 1d40ef04d7ec
children d8baf7dafbd8
files saxswaxs/pipeline.yaml saxswaxs/reduce.xml
diffstat 2 files changed, 6 insertions(+), 26 deletions(-) [+]
line wrap: on
line diff
--- a/saxswaxs/pipeline.yaml	Tue May 30 15:18:46 2023 +0000
+++ b/saxswaxs/pipeline.yaml	Tue May 30 18:03:00 2023 +0000
@@ -1,30 +1,12 @@
 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:
+  - pipeline.MultiplePipelineItem:
+      items:
+        - common.YAMLReader:
             filename: map.yaml
             schema: MapConfig
-        - YAMLReader:
+        - common.YAMLReader:
             filename: integration.yaml
             schema: IntegrationConfig
   - common.IntegrateMapProcessor
--- a/saxswaxs/reduce.xml	Tue May 30 15:18:46 2023 +0000
+++ b/saxswaxs/reduce.xml	Tue May 30 18:03:00 2023 +0000
@@ -1,7 +1,7 @@
 <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="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>
@@ -16,14 +16,12 @@
         <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>