diff woundhealing.xml @ 0:8948cc562b7c draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 4d4d0b10eb6be3b1f13b2becc8f057ac41d3f0de

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/woundhealing.xml	Thu Feb 29 17:43:50 2024 +0000
@@ -0,0 +1,61 @@
+<tool id="woundhealing_scratch_assay" name="Wound healing scratch assay" version="@VERSION@+galaxy0" profile="23.1">
+    <description>image analysis</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive">
+    <![CDATA[
+    mkdir -p ./input &&
+
+    #if $con_input_type.input_type =="yes"
+        tar -C ./input -xvf $con_input_type.input_images &&
+    #else
+        #for $i, $filename in enumerate($con_input_type.input_images):
+            ln -s '$filename' './input/${filename.element_identifier}' &&
+        #end for
+    #end if
+    ImageJ --ij2 --headless 
+    --run '$__tool_directory__/measureWoundClosing.groovy'
+    'inputDir="./input",datasetId="$dataset_id",threshold="$threshold",headless="true",saveResults="true",outDirName="./output"'
+    ]]>
+    </command>
+    <inputs>
+        <conditional name="con_input_type">
+            <param name="input_type" type="select" label="Are the input images packed into a tar archive?">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param> 
+            <when value="no">
+                <param name="input_images" type="data" multiple="true" format="@FORMATS@" label="Images" />
+            </when>
+            <when value="yes">
+                <param name="input_images" type="data" format="tar" label="A tarball of images" />
+            </when>
+        </conditional>
+        <param name="dataset_id" type="text" label="Dataset ID" />
+        <param name="threshold"  type="text" label="CoV threshold (-1: auto)" value="-1"/>
+    </inputs>
+    <outputs>
+        <data name="tif_output" format="tif" from_work_dir="output/*.tif" label="movie output ${on_string}" />
+	<data name="csv_output" format="tabular" from_work_dir="output/*.csv" label="tabular output"/>
+    </outputs>
+    <tests>
+        <test >
+            <conditional name="con_input_type">
+                <param name="input_type" value="no" />
+                <param name="input_images" location="https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/input/A3ROI2_Slow_0000.tif,https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/input/A3ROI2_Slow_0002.tif" />
+	    </conditional>
+	    <param name="dataset_id" value="A3ROI2_Slow" />
+	    <output name="tif_output" location="https://github.com/sunyi000/wound-healing-htm-screen/raw/main/assets/data/A3ROI2_Slow.tif"/>
+	    <output name="csv_output" file="A3ROI2_Slow.csv"/>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+            **What it does**
+            Automated quantification of wound healing in high-throughput time-lapse transmission microscopy scratch assays.
+        ]]>
+    </help>
+    <expand macro="citations" />
+</tool>