changeset 62:2679014bb6eb draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit e280dd942513f966a9a61a3af68ee7972fb8992f-dirty

--- a/saxswaxs/ignoreshed.yml	Thu Apr 13 12:18:11 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-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

--- a/saxswaxs/klspipeline.yaml	Thu Apr 13 12:18:11 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/tomo/pipeline_reduce_nexus.yaml	Thu Apr 13 12:18:11 2023 +0000
+++ b/tomo/pipeline_reduce_nexus.yaml	Thu Apr 13 12:40:41 2023 +0000
@@ -8,7 +8,9 @@
         - YAMLReader:
             filename: reduce.yaml
             schema: TomoReduceConfig
-  - tomo.TomoDataProcessor
+  - tomo.TomoDataProcessor:
+      output_folder: tomo_reduce_plots
+      save_figs: 'only'
   - common.NexusWriter:
       filename: output.nex
       force_overwrite: true

--- a/tomo/pipeline_reduce_yaml.yaml	Thu Apr 13 12:18:11 2023 +0000
+++ b/tomo/pipeline_reduce_yaml.yaml	Thu Apr 13 12:40:41 2023 +0000
@@ -9,7 +9,9 @@
         - YAMLReader:
             filename: reduce.yaml
             schema: TomoReduceConfig
-  - tomo.TomoDataProcessor
+  - tomo.TomoDataProcessor:
+      output_folder: tomo_reduce_plots
+      save_figs: 'only'
   - common.NexusWriter:
       filename: output.nex
       force_overwrite: true

--- a/tomo/tomo_macros.xml	Thu Apr 13 12:18:11 2023 +0000
+++ b/tomo/tomo_macros.xml	Thu Apr 13 12:40:41 2023 +0000
@@ -1,10 +1,10 @@
 <macros>
     <token name="@TOOL_VERSION@">0.1.0</token>
     <token name="@PROFILE@">21.09</token>
-    <token name="@PYTHON_TEMPLATE_VERSION@">3.9.13</token>
+    <token name="@PYTHON_TEMPLATE_VERSION@">3.9</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.0.3">chessanalysispipeline</requirement>
+            <requirement type="package" version="0.0.4">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>

--- a/tomo/tomo_reduce.xml	Thu Apr 13 12:18:11 2023 +0000
+++ b/tomo/tomo_reduce.xml	Thu Apr 13 12:40:41 2023 +0000
@@ -7,32 +7,33 @@
     <command detect_errors="exit_code">
         <![CDATA[
         mkdir tomo_reduce_plots;
-        pip --exists-action i install certif-pyspec==1.5.3 &&
-        #if str($map.type_selector) == "YAML"
-            cp '$input_file' map.yaml &&
+        $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
+        #if str($map.type_selector) == "yaml"
+            cp $input_file map.yaml &&
+            cat $__tool_directory__/andor2.yaml $tool_config > reduce.yaml &&
         #else
-            cp '$input_file' setup.nex &&
+            cp $input_file setup.nex &&
+            cp $tool_config reduce.yaml &&
         #end if
-        cp '$tool_config' reduce.yaml &&
         CHAP --config 
-        #if str($map.type_selector) == "YAML"
-            '$__tool_directory__/pipeline_reduce_yaml.yaml'
+        #if str($map.type_selector) == "yaml"
+            $__tool_directory__/pipeline_reduce_yaml.yaml
         #else
-            '$__tool_directory__/pipeline_reduce_nexus.yaml'
+            $__tool_directory__/pipeline_reduce_nexus.yaml
         #end if
         ]]>
     </command>
     <configfiles>
         <configfile name="tool_config">
             <![CDATA[#slurp
-                #echo 'img_x_bounds:' #
-                #if str($img_x_bounds.type_selector) == "full_range"
-                    #echo '- -1'
-                    #echo '- -1'
-                #else
-                    #echo '- ' + str($img_x_bounds.low)
-                    #echo '- ' + str($img_x_bounds.upp)
-                #end if
+#echo 'img_x_bounds:' #
+#if str($img_x_bounds.type_selector) == "full_range"
+#echo '- -1' #
+#echo '- -1' #
+#else
+#echo '- ' + str($img_x_bounds.low) #
+#echo '- ' + str($img_x_bounds.upp) #
+#end if
             ]]>
         </configfile>
     </configfiles>