Mercurial > repos > iuc > imagej2_convert_format
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 @@ -0,0 +1,71 @@ +<?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>
