# HG changeset patch
# User ximgchess
# Date 1681300608 0
# Node ID 33506016d5fe15f645cb34e0662189206da3b867
# Parent  85d802ce6856c70f93cab9acbd90c163c12183d5
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 3e8c1c54d5e12fdbc4f6c5cdae88b6d054db7c45-dirty

diff -r 85d802ce6856 -r 33506016d5fe tomo/.tomo_reduce.xml.swp
Binary file tomo/.tomo_reduce.xml.swp has changed
diff -r 85d802ce6856 -r 33506016d5fe tomo/tmp.tmp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo/tmp.tmp	Wed Apr 12 11:56:48 2023 +0000
@@ -0,0 +1,95 @@
+<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[
+        #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 $tool_config reduce.yaml &&
+        #end if
+        cat reduce.yaml
+        ]]>
+    </command>
+    <configfiles>
+        <configfile name="tool_config">
+            <![CDATA[#slurp
+#*
+#if str($map.type_selector) == "yaml"
+#echo 'detector:' #
+#echo '  file: ' + str($__tool_directory__) + '/andor2.yaml' #
+#end if
+*#
+#echo 'img_x_bounds:' #
+#if str($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>
+    <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">andor2</option>
+                        <option value="manta">manta</option>
+                        <option value="retiga">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 85d802ce6856 -r 33506016d5fe tomo/tomo_reduce.xml
--- a/tomo/tomo_reduce.xml	Wed Apr 12 11:49:09 2023 +0000
+++ b/tomo/tomo_reduce.xml	Wed Apr 12 11:56:48 2023 +0000
@@ -8,21 +8,23 @@
         <![CDATA[
         #if str($map.type_selector) == "yaml"
             cp $input_file map.yaml &&
-            cat $__tool_directory__/andor2.yaml $tool_config > reduce.yaml &&
+            cp $__tool_directory__/andor2.yaml reduce.yaml &&
         #else
             cp $input_file setup.nex &&
-            cp $tool_config reduce.yaml &&
         #end if
+        $tool_config >> reduce.yaml &&
         cat reduce.yaml
         ]]>
     </command>
     <configfiles>
         <configfile name="tool_config">
             <![CDATA[#slurp
+#*
 #if str($map.type_selector) == "yaml"
 #echo 'detector:' #
-#echo '  file:' + str($__tool_directory__) +'/andor2.yaml' #
+#echo '  file: ' + str($__tool_directory__) + '/andor2.yaml' #
 #end if
+*#
 #echo 'img_x_bounds:' #
 #if str($img_x_bounds.type_selector) == "full_range"
 #echo '- -1' #