changeset 60:3a9135044f14 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit eda217fb0afe5af50380a24b578c668db9c004f4-dirty

Binary file tomo/.tmp.tmp.swp has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo/tmp.tmp	Wed Apr 12 19:04:05 2023 +0000
@@ -0,0 +1,84 @@
+<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[
+        $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
+        ls -alh $__tool_directory__/.. &&
+        cp $tool_config reduce.yaml
+        ]]>
+    </command>
+    <configfiles>
+        <configfile name="tool_config">
+            <![CDATA[#slurp
+#*
+#if str($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"/>
+    </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>

--- a/tomo/tomo_reduce.xml	Wed Apr 12 18:58:32 2023 +0000
+++ b/tomo/tomo_reduce.xml	Wed Apr 12 19:04:05 2023 +0000
@@ -6,20 +6,26 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
+        mkdir tomo_reduce_plots;
         $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
-        ls -alh $__tool_directory__/.. &&
-        cp $tool_config reduce.yaml
+        #if str($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 $tool_config reduce.yaml &&
+        #end if
+        CHAP --config 
+        #if str($map.type_selector) == "yaml"
+            $__tool_directory__/pipeline_reduce_yaml.yaml
+        #else
+            $__tool_directory__/pipeline_reduce_nexus.yaml
+        #end if
         ]]>
     </command>
     <configfiles>
         <configfile name="tool_config">
             <![CDATA[#slurp
-#*
-#if str($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' #
@@ -68,6 +74,10 @@
     </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[