Mercurial > repos > imgteam > imagej2_bunwarpj_compare_raw

comparison imagej2_bunwarpj_compare_raw.xml @ 1:9349961e09ce draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:50:39 +0000
parents d17be9aef142
children 77411a986a70
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0:d17be9aef142 1:9349961e09ce
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_bunwarpj_compare_raw" name="Compare two raw deformations" version="@WRAPPER_VERSION@.0"> 1 <tool id="imagej2_bunwarpj_compare_raw" name="Compare two raw deformations" version="@WRAPPER_VERSION@.0">
3 <description>by warping index with bUnwarpJ</description> 2 <description>by warping index with bUnwarpJ</description>
4 <macros> 3 <macros>
5 <import>imagej2_macros.xml</import> 4 <import>imagej2_macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="fiji_requirements" /> 6 <expand macro="fiji_requirements"/>
8 <command> 7 <command detect_errors="exit_code"><![CDATA[
9 <![CDATA[ 8 #import os
10 python $__tool_directory__/imagej2_bunwarpj_compare_raw.py 9 #set output_log = 'output_log.txt'
11 --target_image "$target_image" 10 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
12 --target_image_format $target_image.ext 11 #set source_with_ext = '.'.join([source_sans_ext, $source_image.ext])
13 --source_image "$source_image" 12 ln -s '$source_image.file_name' '$source_with_ext' &&
14 --source_image_format $source_image.ext 13 #set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
15 --target_raw_transformation "$target_raw_transformation" 14 #set target_with_ext = '.'.join([target_sans_ext, $target_image.ext])
16 --source_raw_transformation "$source_raw_transformation" 15 ln -s '$target_image.file_name' '$target_with_ext' &&
17 --output "$output" 16 bunwarpj -compare_raw
18 ]]> 17 '$target_with_ext'
19 </command> 18 '$source_with_ext'
19 '$target_raw_transformation'
20 '$source_raw_transformation'
21 &>'$output_log';
22 if [[ $? -ne 0 ]]; then
23 cat '$output_log' >&2;
24 else
25 grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output';
26 fi
27 ]]></command>
20 <inputs> 28 <inputs>
21 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/> 29 <expand macro="param_target_image"/>
22 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/> 30 <expand macro="param_source_image"/>
23 <param format="txt" name="target_raw_transformation" type="data" label="Raw transformation file 1"/> 31 <param format="txt" name="target_raw_transformation" type="data" label="Raw transformation file 1"/>
24 <param format="txt" name="source_raw_transformation" type="data" label="Raw transformation file 2"/> 32 <param format="txt" name="source_raw_transformation" type="data" label="Raw transformation file 2"/>
25 </inputs> 33 </inputs>
26 <outputs> 34 <outputs>
27 <data name="output" format="txt" label="${tool.name} (same direction) on ${on_string}: Warping index" /> 35 <data name="output" format="txt" label="${tool.name} (same direction) on ${on_string}"/>
28 </outputs> 36 </outputs>
29 <tests> 37 <tests>
30 <test> 38 <test>
31 <param name="target_image" value="dotblot.jpg" /> 39 <expand macro="test_bunwarpj_raw_transform"/>
32 <param name="source_image" value="blobs.gif" /> 40 <output name="output" file="warping_index1.txt" compare="contains"/>
33 <param name="target_raw_transformation" value="target_raw_transformation.txt" />
34 <param name="source_raw_transformation" value="source_raw_transformation.txt" />
35 <output name="output" file="warping_index1.txt" compare="contains" />
36 </test> 41 </test>
37 <test> 42 <test>
38 <param name="target_image" value="dotblot.jpg" /> 43 <expand macro="test_target_source_images"/>
39 <param name="source_image" value="blobs.gif" /> 44 <param name="target_raw_transformation" value="source_raw_transformation.txt"/>
40 <param name="target_raw_transformation" value="source_raw_transformation.txt" /> 45 <param name="source_raw_transformation" value="source_raw_transformation.txt"/>
41 <param name="source_raw_transformation" value="source_raw_transformation.txt" /> 46 <output name="output" file="warping_index2.txt"/>
42 <output name="output" file="warping_index2.txt" />
43 </test> 47 </test>
44 </tests> 48 </tests>
45 <help> 49 <help>
46 **What it does** 50 **What it does**
47 51
51 **Convert elastic transformation to raw** tool. 55 **Convert elastic transformation to raw** tool.
52 56
53 ]]> 57 ]]>
54 58
55 </help> 59 </help>
56 <expand macro="bunwarpj_citations" /> 60 <expand macro="bunwarpj_citations"/>
57 </tool> 61 </tool>