# HG changeset patch
# User watsocam
# Date 1648659389 0
# Node ID 46b897eb2c8ea6a68da3ce05696f151ee3a07d48
# Parent  aba3655fdef07071e2e7822aaaa7bc8694300786
"planemo upload for repository https://github.com/ohsu-comp-bio/quantification commit 150f21e52974f99ec39bf92d9e7e611861860d0f"

diff -r aba3655fdef0 -r 46b897eb2c8e quantification.xml
--- a/quantification.xml	Fri Mar 11 23:35:52 2022 +0000
+++ b/quantification.xml	Wed Mar 30 16:56:29 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="quantification" name="Quantification" version="@VERSION@.5" profile="17.09">
+<tool id="quantification" name="Quantification" version="@VERSION@.6" profile="17.09">
     <description>Single cell quantification, a module for single-cell data extraction given a segmentation mask and multi-channel image.</description>
     <macros>
         <import>macros.xml</import>
@@ -8,28 +8,26 @@
     @VERSION_CMD@
 
     <command detect_errors="exit_code"><![CDATA[
-    ln -s '$image' '${image.name}'.ome.tiff;
-    ln -s '$primary_mask' '${primary_mask.name}'.ome.tiff; 
-    #for $mask in $supp_masks:
-    ln -s '$mask' '${mask.name}'.ome.tiff;
-    #end for
+    ln -s $image input.ome.tiff;
+    ln -s $primary_mask primary_mask.tiff;
+    #if $supp_masks
+    ln -s $supp_masks supp_mask.tiff;
+    #end if
 
     mkdir ./tool_out;
 
     @CMD_BEGIN@
-    
+
     python \$QUANT_PATH
-    --masks 
-    '${primary_mask.name}'.ome.tiff
+    --masks
+    primary_mask.tiff
     #if $supp_masks
-    #for $mask in $supp_masks:
-    '${mask.name}'.ome.tiff
-    #end for
+    supp_mask.tiff
     #end if
 
-    --image '${image.name}'.ome.tiff
+    --image input.ome.tiff
     --output ./tool_out
-   
+
     #if $mask_props
     --mask_props $mask_props
     #end if
@@ -39,22 +37,22 @@
 
     --channel_names '$channel_names';
 
-    cp tool_out/*cellMasks.csv cellMasks.csv
+    cp tool_out/*primary_mask.csv primary_mask.csv
     ]]></command>
 
     <inputs>
         <param name="image" type="data" format="tiff" label="Registered TIFF"/>
         <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="supp_masks" type="data" 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="cellmask" from_work_dir="cellMasks.csv" label="CellMaskQuant"/>
+        <data format="csv" name="cellmask" from_work_dir="primary_mask.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"/>
+          <discover_datasets pattern="__designation_and_ext__" format="csv" directory="tool_out/" visible="true"/>
         </collection>
      </outputs>
     <help><![CDATA[