Mercurial > repos > imgteam > imagej2_create_image
diff imagej2_create_image.xml @ 1:1a7c29d5fc11 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
---|---|
date | Mon, 28 Sep 2020 16:43:06 +0000 |
parents | dc3935a0165a |
children | 666af1279007 |
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--- a/imagej2_create_image.xml Tue Sep 17 16:57:52 2019 -0400 +++ b/imagej2_create_image.xml Mon Sep 28 16:43:06 2020 +0000 @@ -1,51 +1,55 @@ -<?xml version='1.0' encoding='UTF-8'?> <tool id="imagej2_create_image" name="Create new image" version="@WRAPPER_VERSION@.0"> <description></description> <macros> <import>imagej2_macros.xml</import> </macros> - <expand macro="fiji_requirements" /> - <command> -<![CDATA[ - python $__tool_directory__/imagej2_create_image.py - --width $width - --height $height - --depth $depth - --image_type $image_type - --image_title "$image_title" - --jython_script $__tool_directory__/imagej2_create_image_jython_script.py - --output_datatype $output_datatype - --out_fname "$output" -]]> - </command> + <expand macro="fiji_requirements"/> + <command detect_errors="exit_code"><![CDATA[ +#set output_log = '$output_log.txt' +#set output_name = '.'.join(['new_image', str($output_datatype)]) +ImageJ --ij2 --headless --debug +--jython '$__tool_directory__/imagej2_create_image_jython_script.py' +'$image_title' +$width +$height +$depth +'$image_type' +'$output_name' +&>'$output_log'; +if [[ $? -ne 0 ]]; then + cat '$output_log' >&2; +else + mv '$output_name' '$output'; +fi +]]></command> <inputs> - <expand macro="image_type" /> - <param name="image_title" type="text" label="Image title" help="Leave blank for no title" /> - <param name="width" type="integer" value="512" min="1" label="Image width in pixels" /> - <param name="height" type="integer" value="512" min="1" label="Image height in pixels" /> - <param name="depth" type="integer" value="1" min="1" label="Image depth" help="Specifies the number of stack slices" /> + <expand macro="image_type"/> + <param name="image_title" type="text" label="Image title" help="Leave blank for no title"/> + <param name="width" type="integer" value="512" min="1" label="Image width in pixels"/> + <param name="height" type="integer" value="512" min="1" label="Image height in pixels"/> + <param name="depth" type="integer" value="1" min="1" label="Image depth" help="Specifies the number of stack slices"/> <param name="output_datatype" type="select" label="Save as format"> - <expand macro="image_datatypes" /> + <expand macro="image_datatypes"/> </param> </inputs> <outputs> <data name="output" format="jpg"> <actions> <action type="format"> - <option type="from_param" name="output_datatype" /> + <option type="from_param" name="output_datatype"/> </action> </actions> </data> </outputs> <tests> <test> - <param name="image_type" value="8-bit_ramp" /> - <param name="image_title" value="MyTitle" /> - <param name="width" value="256" /> - <param name="height" value="256" /> - <param name="depth" value="1" /> - <param name="output_datatype" value="jpg" /> - <output name="output" file="create_image1.jpg" ftype="jpg" /> + <param name="image_type" value="8-bit_ramp"/> + <param name="image_title" value="MyTitle"/> + <param name="width" value="256"/> + <param name="height" value="256"/> + <param name="depth" value="1"/> + <param name="output_datatype" value="jpg"/> + <output name="output" file="create_image1.jpg" ftype="jpg"/> </test> </tests> <help> @@ -63,5 +67,5 @@ ]]> </help> - <expand macro="fiji_headless_citations" /> + <expand macro="fiji_headless_citations"/> </tool>