diff tomo/tomo_reduce.xml @ 105:4205395a6091 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 6697892ecc504b00077394d0c167431ec3ac12f7-dirty

--- a/tomo/tomo_reduce.xml	Thu May 25 12:44:16 2023 +0000
+++ b/tomo/tomo_reduce.xml	Fri May 26 13:48:39 2023 +0000
@@ -29,6 +29,16 @@
     <configfiles>
         <configfile name="tool_config">
             <![CDATA[#slurp
+#if str($map.detector.type_selector) == "manual"
+#echo 'detector:' #
+#echo '  prefix: $prefix' #
+#echo '  rows: str($rows)' #
+#echo '  columns: str($columns)' #
+#echo '  pixel_size:' #
+#echo '  - ' + str($x_pixelsize) #
+#echo '  - ' + str($y_pixelsize) #
+#echo '  lens_magnification: str($lens_magnification)' #
+#end if
 #echo 'img_x_bounds:' #
 #if str($img_x_bounds.type_selector) == "full_range"
 #echo '- -1' #
@@ -53,11 +63,20 @@
                         <option value="andor2.yaml">andor2</option>
                         <option value="manta.yaml">manta</option>
                         <option value="retiga.yaml">retiga</option>
+                        <option value="manual">enter manually</option>
                         <option value="from_file">from file</option>
                     </param>
                     <when value="andor2.yaml"/>
                     <when value="manta.yaml"/>
                     <when value="retiga.yaml"/>
+                    <when value="manual">
+                        <param name="prefix" type="text" label="Detector prefix in SPEC file"/>
+                        <param name="rows" type="integer" optional="false" label="Number of pixel rows on detector"/>
+                        <param name="columns" type="integer" optional="false" label="Number of pixel columns on detector"/>
+                        <param name="x_pixelsize" type="float" optional="false" label="Row pixel size of detector in mm"/>
+                        <param name="y_pixelsize" type="float" optional="false" label="Column pixel size of detector in mm"/>
+                        <param name="lens_magnification" type="float" value="1.0" optional="true" label="Detector lens magnification"/>
+                    </when>
                     <when value="from_file">
                         <param name="detector_file" type="data" format="yaml" optional="false" label="Detector config file"/>
                     </when>