Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw

diff imagej2_bunwarpj_convert_to_raw.xml @ 0:95fb6fa70c2f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author imgteam
date Tue, 17 Sep 2019 17:06:56 -0400
parents
children 7f9840d3b7e7
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_bunwarpj_convert_to_raw.xml	Tue Sep 17 17:06:56 2019 -0400
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+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="imagej2_bunwarpj_convert_to_raw" name="Convert elastic transformation to raw" version="@WRAPPER_VERSION@.0">
+    <description>with bUnwarpJ</description>
+    <macros>
+        <import>imagej2_macros.xml</import>
+    </macros>
+    <expand macro="fiji_requirements" />
+    <command>
+<![CDATA[
+    python $__tool_directory__/imagej2_bunwarpj_convert_to_raw.py
+    --target_image "$target_image"
+    --target_image_format $target_image.ext
+    --source_image "$source_image"
+    --source_image_format $source_image.ext
+    --elastic_transformation "$elastic_transformation"
+    --raw_transformation "$raw_transformation"
+]]>
+    </command>
+    <inputs>
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/>
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/>
+        <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy -->
+        <param format="txt" name="elastic_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in elastic format"/>
+    </inputs>
+    <outputs>
+        <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy -->
+        <data name="raw_transformation" format="txt" label="${tool.name} on ${on_string}: Raw transformation" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="target_image" value="dotblot.jpg" />
+            <param name="source_image" value="blobs.gif" />
+            <param name="elastic_transformation" value="source_elastic_transformation.txt" ftype="txt" />
+            <output name="raw_transformation" file="source_raw_transformation.txt" ftype="txt" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+<![CDATA[
+Converts an elastic (i.e., B-spline ) transformation file into a raw transformation file.  The elastic
+transformation file must be in the same format as the files created with the **Save Transformation**
+option in the **Align two images with bUnwarpJ** tool.
+
+]]>
+
+    </help>
+    <expand macro="bunwarpj_citations" />
+</tool>