diff quantification.xml @ 1:aba3655fdef0 draft

"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 897a7dc7cb43e45d6f0fdfe2b2970e59f20f8853"

--- a/quantification.xml	Fri Mar 12 00:19:24 2021 +0000
+++ b/quantification.xml	Fri Mar 11 23:35:52 2022 +0000
@@ -18,6 +18,7 @@
 
     @CMD_BEGIN@
     
+    python \$QUANT_PATH
     --masks 
     '${primary_mask.name}'.ome.tiff
     #if $supp_masks
@@ -28,9 +29,17 @@
 
     --image '${image.name}'.ome.tiff
     --output ./tool_out
+   
+    #if $mask_props
+    --mask_props $mask_props
+    #end if
+    #if $intensity_props
+    --intensity_props $intensity_props
+    #end if
+
     --channel_names '$channel_names';
 
-    mv ./tool_out/*.csv ./tool_out/quantified.csv;
+    cp tool_out/*cellMasks.csv cellMasks.csv
     ]]></command>
 
     <inputs>
@@ -38,11 +47,16 @@
         <param name="primary_mask" type="data" format="tiff" label="Primary Cell Mask"/>
         <param name="supp_masks" type="data" multiple="true" optional="true" format="tiff" label="Additional Cell Masks"/>
         <param name="channel_names" type="data" format="csv" label="Marker Channels"/>
+        <param name="mask_props" type="text" label="Mask Metrics" help="Space separated list of additional metrics to be calculated for every mask."/>
+        <param name="intensity_props" type="text" label="Intensity Metrics" help="Space separated list of additional metrics to be calculated for every marker separately."/>
     </inputs>
 
     <outputs>
-        <data format="csv" name="quant_out" from_work_dir="./tool_out/quantified.csv" label="${tool.name} on ${on_string}"/>
-    </outputs>
+        <data format="csv" name="cellmask" from_work_dir="cellMasks.csv" label="CellMaskQuant"/>
+        <collection type="list" name="quantification" label="${tool.name} on ${on_string}">
+            <discover_datasets pattern="__designation_and_ext__" format="csv" directory="tool_out/" visible="true"/>
+        </collection>
+     </outputs>
     <help><![CDATA[
 # Single cell quantification
 Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output.