diff macros.xml @ 1:aba3655fdef0 draft

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

--- a/macros.xml	Fri Mar 12 00:19:24 2021 +0000
+++ b/macros.xml	Fri Mar 11 23:35:52 2022 +0000
@@ -2,12 +2,13 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.6.10">python</requirement>
-            <requirement type="package" version="0.17.2">scikit-image</requirement>
-            <requirement type="package" version="2.10.0">h5py</requirement>
-            <requirement type="package" version="1.0.4">pandas</requirement>
-            <requirement type="package" version="1.18.5">numpy</requirement>
-            <requirement type="package" version="1.0.1">pathlib</requirement>
+            <container type="docker">labsyspharm/quantification:@VERSION@</container>
+            <requirement type="package" version="3.9">python</requirement>
+            <requirement type="package" version="0.18.0">scikit-image</requirement>
+            <requirement type="package">h5py</requirement>
+            <requirement type="package">pandas</requirement>
+            <requirement type="package">numpy</requirement>
+            <requirement type="package">pathlib</requirement>
         </requirements>
     </xml>
 
@@ -19,6 +20,13 @@
         </citations>
     </xml>
 
-    <token name="@VERSION@">1.3.1</token>
-    <token name="@CMD_BEGIN@">python ${__tool_directory__}/CommandSingleCellExtraction.py</token>
+    <token name="@VERSION@">1.5.1</token>
+    <token name="@CMD_BEGIN@"><![CDATA[
+    QUANT_PATH="";
+    if [ -f "/app/CommandSingleCellExtraction.py" ]; then
+        export QUANT_PATH="/app/CommandSingleCellExtraction.py";
+    else
+        export QUANT_PATH="${__tool_directory__}/CommandSingleCellExtraction.py";
+    fi;
+    ]]></token>
 </macros>