diff imagej2_convert_format.xml @ 0:312e8ce708b1 draft

planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
author iuc
date Tue, 09 Jun 2015 12:21:40 -0400
parents
children 14d09b0ab9e1
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_convert_format.xml	Tue Jun 09 12:21:40 2015 -0400
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+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="imagej2_convert_format" name="Convert image format" version="1.0.0">
+    <description>with bioformats</description>
+    <macros>
+        <import>imagej2_macros.xml</import>
+    </macros>
+    <expand macro="python_bioformats_requirements" />
+    <command interpreter="python">
+<![CDATA[
+        imagej2_convert_format.py
+        --in_fname "$input"
+        --input_datatype $input.ext
+        --max_heap_size_type $set_max_heap_size.max_heap_size_type
+        --max_heap_size $set_max_heap_size.max_heap_size
+        --output_datatype $output_datatype
+        --out_fname "$output"
+]]>
+    </command>
+    <inputs>
+        <expand macro="max_heap_size_type_conditional" />
+        <param format="bmp,eps,gif,html,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
+        <param name="output_datatype" type="select" label="Convert to format">
+            <option value="jpg" selected="true">jpg</option>
+            <option value="png">png</option>
+            <option value="tiff">tiff</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="jpg">
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="output_datatype" />
+                 </action>
+           </actions>
+       </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="dot_blot.jpg" ftype="jpg" />
+            <param name="max_heap_size_type" value="megabytes" />
+            <param name="max_heap_size" value="256" />
+            <param name="input_datatype" value="jpg" />
+            <param name="output_datatype" value="png" />
+            <output name="output" file="dot_blot.png" ftype="png" />
+        </test>
+        <test>
+            <param name="input" value="dot_blot.png" ftype="png" />
+            <param name="input_datatype" value="png" />
+            <param name="output_datatype" value="tiff" />
+            <output name="output" file="dot_blot.tiff" ftype="tiff" />
+        </test>
+        <test>
+            <param name="input" value="dot_blot.tiff" ftype="tiff" />
+            <param name="input_datatype" value="tiff" />
+            <param name="output_datatype" value="jpg" />
+            <output name="output" file="dot_blot.jpg" ftype="jpg" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+<![CDATA[
+Converts an image file from one format to another where supported input and output formats are the
+intersection of the relative formats supported by both Galaxy and Bioformats.
+
+Go `here <https://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html>`_ for Bioformats image formats.
+]]>
+
+    </help>
+    <expand macro="citations" />
+</tool>