# HG changeset patch
# User ximgchess
# Date 1682945446 0
# Node ID 7638a2c68b7f587464e51b14696c54707c8ac41d
# Parent  d0bc5f9dc4c9cbf15e3a51d91ff6db27d9aa29d3
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty

diff -r d0bc5f9dc4c9 -r 7638a2c68b7f tomo/tomo_reduce.bu
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo/tomo_reduce.bu	Mon May 01 12:50:46 2023 +0000
@@ -0,0 +1,94 @@
+<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;
+        $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
+        #if str($map.type_selector) == "yaml"
+            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"/>
+                    <when value="manta"/>
+                    <when value="retiga"/>
+                </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>
diff -r d0bc5f9dc4c9 -r 7638a2c68b7f tomo/tomo_reduce.xml
--- a/tomo/tomo_reduce.xml	Thu Apr 27 11:01:04 2023 +0000
+++ b/tomo/tomo_reduce.xml	Mon May 01 12:50:46 2023 +0000
@@ -10,16 +10,10 @@
         $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
         #if str($map.type_selector) == "yaml"
             cp $input_file map.yaml &&
-            cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.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
+            cp $tool_config reduce.yaml
         #end if
         ]]>
     </command>
@@ -51,9 +45,9 @@
                         <option value="manta.yaml">manta</option>
                         <option value="retiga.yaml">retiga</option>
                     </param>
-                    <when value="andor2"/>
-                    <when value="manta"/>
-                    <when value="retiga"/>
+                    <when value="andor2.yaml"/>
+                    <when value="manta.yaml"/>
+                    <when value="retiga.yaml"/>
                 </conditional>
             </when>
             <when value="nexus">