# HG changeset patch
# User ximgchess
# Date 1684929425 0
# Node ID 72608a06dd7fa797770740253cdfb54721e28d93
# Parent  b930f59f334c198fed302c6746b1dfc2667f2956
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 01388c69776c82e48e84676a3d17d4623f5e08bd-dirty

diff -r b930f59f334c -r 72608a06dd7f tomo/pipeline_combine.yaml
--- a/tomo/pipeline_combine.yaml	Wed May 24 11:14:21 2023 +0000
+++ b/tomo/pipeline_combine.yaml	Wed May 24 11:57:05 2023 +0000
@@ -1,11 +1,11 @@
 pipeline:
 
   # Combine tomography stacks
-  - common.MultipleReader:
-      readers:
-        - NexusReader:
+  - pipeline.MultiplePipelineItem:
+      items:
+        - common.NexusReader:
             filename: reconstructed.nex
-        - YAMLReader:
+        - common.YAMLReader:
             filename: combine.yaml
             schema: TomoCombineConfig
   - tomo.TomoDataProcessor:
diff -r b930f59f334c -r 72608a06dd7f tomo/pipeline_find_center.yaml
--- a/tomo/pipeline_find_center.yaml	Wed May 24 11:14:21 2023 +0000
+++ b/tomo/pipeline_find_center.yaml	Wed May 24 11:57:05 2023 +0000
@@ -1,11 +1,11 @@
 pipeline:
 
   # Find rotation axis centers for the tomography stacks
-  - common.MultipleReader:
-      readers:
-        - NexusReader:
+  - pipeline.MultiplePipelineItem:
+      items:
+        - common.NexusReader:
             filename: reduced.nex
-        - YAMLReader:
+        - common.YAMLReader:
             filename: find_center.yaml
             schema: TomoFindCenterConfig
   - tomo.TomoDataProcessor:
diff -r b930f59f334c -r 72608a06dd7f tomo/pipeline_reconstruct.yaml
--- a/tomo/pipeline_reconstruct.yaml	Wed May 24 11:14:21 2023 +0000
+++ b/tomo/pipeline_reconstruct.yaml	Wed May 24 11:57:05 2023 +0000
@@ -1,14 +1,14 @@
 pipeline:
 
   # Reconstruct tomography stacks
-  - common.MultipleReader:
-      readers:
-        - NexusReader:
+  - pipeline.MultiplePipelineItem:
+      items:
+        - common.NexusReader:
             filename: reduced.nex
-        - YAMLReader:
+        - common.YAMLReader:
             filename: reconstruct.yaml
             schema: TomoReconstructConfig
-        - YAMLReader:
+        - common.YAMLReader:
             filename: centers.yaml
             schema: TomoFindCenterConfig
   - tomo.TomoDataProcessor:
diff -r b930f59f334c -r 72608a06dd7f tomo/pipeline_reduce_nexus.yaml
--- a/tomo/pipeline_reduce_nexus.yaml	Wed May 24 11:14:21 2023 +0000
+++ b/tomo/pipeline_reduce_nexus.yaml	Wed May 24 11:57:05 2023 +0000
@@ -1,11 +1,11 @@
 pipeline:
 
   # Reduce tomography images
-  - common.MultipleReader:
-      readers:
-        - NexusReader:
+  - pipeline.MultiplePipelineItem:
+      items:
+        - common.NexusReader:
             filename: setup.nex
-        - YAMLReader:
+        - common.YAMLReader:
             filename: reduce.yaml
             schema: TomoReduceConfig
   - tomo.TomoDataProcessor:
diff -r b930f59f334c -r 72608a06dd7f tomo/pipeline_reduce_yaml.yaml
--- a/tomo/pipeline_reduce_yaml.yaml	Wed May 24 11:14:21 2023 +0000
+++ b/tomo/pipeline_reduce_yaml.yaml	Wed May 24 11:57:05 2023 +0000
@@ -1,12 +1,12 @@
 pipeline:
 
   # Reduce tomography images
-  - common.MultipleReader:
-      readers:
-        - YAMLReader:
+  - pipeline.MultiplePipelineItem:
+      items:
+        - common.YAMLReader:
             filename: map.yaml
             schema: MapConfig
-        - YAMLReader:
+        - common.YAMLReader:
             filename: reduce.yaml
             schema: TomoReduceConfig
   - tomo.TomoDataProcessor:
diff -r b930f59f334c -r 72608a06dd7f tomo/tomo_reduce_old.xml
--- a/tomo/tomo_reduce_old.xml	Wed May 24 11:14:21 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-<tool id="CHAP_tomo_reduce" name="Tomo Reduce" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
-    <description>Reduce tomography images</description>
-    <macros>
-        <import>tomo_macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <command detect_errors="exit_code">
-        <![CDATA[
-        mkdir tomo_reduce_plots;
-        #if str($map.type_selector) == "yaml"
-            $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
-            cp $input_file map.yaml &&
-            cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml &&
-        #else
-            cp $input_file setup.nex &&
-            cp $tool_config reduce.yaml &&
-        #end if
-        CHAP --config
-        #if str($map.type_selector) == "yaml"
-            $__tool_directory__/pipeline_reduce_yaml.yaml
-        #else
-            $__tool_directory__/pipeline_reduce_nexus.yaml
-        #end if
-        ]]>
-    </command>
-    <configfiles>
-        <configfile name="tool_config">
-            <![CDATA[#slurp
-#echo 'img_x_bounds:' #
-#if str($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
-            ]]>
-        </configfile>
-    </configfiles>
-    <inputs>
-        <conditional name="map">
-            <param name="type_selector" type="select" display="radio" label="Choose map file type">
-                <option value="yaml">YAML</option>
-                <option value="nexus">NeXus</option>
-            </param>
-            <when value="yaml">
-                <param name="input_file" type="data" format="yaml" optional="false" label="Map config file"/>
-                <conditional name="detector">
-                    <param name="type_selector" type="select" display="radio" label="Choose detector prefix">
-                        <option value="andor2.yaml">andor2</option>
-                        <option value="manta.yaml">manta</option>
-                        <option value="retiga.yaml">retiga</option>
-                    </param>
-                    <when value="andor2.yaml"/>
-                    <when value="manta.yaml"/>
-                    <when value="retiga.yaml"/>
-                </conditional>
-            </when>
-            <when value="nexus">
-                <param name="input_file" type="data" format="nex" optional="false" label="Tomography setup file"/>
-            </when>
-        </conditional>
-        <conditional name="img_x_bounds">
-            <param name="type_selector" type="select" label="Choose vertical detector image bounds">
-                <option value="full_range" selected="true">Use the full image range</option>
-                <option value="enter_range">Manually enter the image range</option>
-            </param>
-            <when value="full_range"/>
-            <when value="enter_range">
-                <param name="low" type="integer" value="-1" optional="false" label="Lower image range index"/>
-                <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index"/>
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/>
-        <collection name="tomo_reduce_plots" type="list" label="Data reduction images">
-            <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/>
-        </collection>
-        <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/>
-    </outputs>
-    <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>
-    <expand macro="citations"/>
-</tool>