changeset 32:21c5d24fb8d8 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 3e8c1c54d5e12fdbc4f6c5cdae88b6d054db7c45-dirty

Binary file tomo/.tomo_reduce.xml.swp has changed

--- a/tomo/tmp.tmp	Wed Apr 12 11:56:48 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,95 +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[
-        #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>

--- a/tomo/tomo_reduce.xml	Wed Apr 12 11:56:48 2023 +0000
+++ b/tomo/tomo_reduce.xml	Wed Apr 12 12:00:22 2023 +0000
@@ -6,14 +6,21 @@
     <expand macro="requirements"/>
     <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 &&
-            cp $__tool_directory__/andor2.yaml reduce.yaml &&
+            cat $__tool_directory__/andor2.yaml $tool_config > reduce.yaml &&
         #else
             cp $input_file setup.nex &&
+            cp $tool_config reduce.yaml &&
         #end if
-        $tool_config >> reduce.yaml &&
-        cat reduce.yaml
+        CHAP --config 
+        #if str($map.type_selector) == "yaml"
+            $__tool_directory__/pipeline_reduce_yaml.yaml
+        #else
+            $__tool_directory__/pipeline_reduce_nexus.yaml
+        #end if
         ]]>
     </command>
     <configfiles>
@@ -73,12 +80,10 @@
     </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[