comparison imagej2_bunwarpj_compare_elastic_raw.xml @ 1:2be338fc671e draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:44:56 +0000
parents 1bffabc15695
children
comparison
equal deleted inserted replaced
0:1bffabc15695 1:2be338fc671e
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_bunwarpj_compare_elastic_raw" name="Compare elastic and raw deformation" version="@WRAPPER_VERSION@.0"> 1 <tool id="imagej2_bunwarpj_compare_elastic_raw" name="Compare elastic and raw deformation" 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 $__tool_directory__/imagej2_bunwarpj_compare_elastic_raw.py 9 #set output_log = 'output_log.txt'
11 --target_image "$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($target_image.file_name))[0]
15 --target_elastic_transformation "$target_elastic_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 "$output" 16 bunwarpj -compare_elastic_raw
18 ]]> 17 '$target_with_ext'
19 </command> 18 '$source_with_ext'
19 '$target_elastic_transformation'
20 '$source_raw_transformation'
21 '$output'
22 &>'$output_log';
23 if [[ $? -ne 0 ]]; then
24 cat '$output_log' >&2;
25 else
26 grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output';
27 fi
28 ]]></command>
20 <inputs> 29 <inputs>
21 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/> 30 <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"/> 31 <expand macro="param_source_image"/>
23 <param format="txt" name="target_elastic_transformation" type="data" label="Elastic transformation file"/> 32 <param format="txt" name="target_elastic_transformation" type="data" label="Elastic transformation file"/>
24 <param format="txt" name="source_raw_transformation" type="data" label="Raw transformation file"/> 33 <param format="txt" name="source_raw_transformation" type="data" label="Raw transformation file"/>
25 </inputs> 34 </inputs>
26 <outputs> 35 <outputs>
27 <data name="output" format="txt" label="${tool.name} (same direction) on ${on_string}: Warping index" /> 36 <data name="output" format="txt" label="${tool.name} (same direction) on ${on_string}"/>
28 </outputs> 37 </outputs>
29 <tests> 38 <tests>
30 <test> 39 <test>
31 <param name="target_image" value="dotblot.jpg" /> 40 <expand macro="test_target_source_images"/>
32 <param name="source_image" value="blobs.gif" /> 41 <param name="target_elastic_transformation" value="target_elastic_transformation.txt"/>
33 <param name="target_elastic_transformation" value="target_elastic_transformation.txt" /> 42 <param name="source_raw_transformation" value="source_raw_transformation.txt"/>
34 <param name="source_raw_transformation" value="source_raw_transformation.txt" /> 43 <output name="output" file="warping_index_raw.txt" compare="contains"/>
35 <output name="output" file="warping_index_raw.txt" compare="contains" />
36 </test> 44 </test>
37 </tests> 45 </tests>
38 <help> 46 <help>
39 **What it does** 47 **What it does**
40 48
46 tool. 54 tool.
47 55
48 ]]> 56 ]]>
49 57
50 </help> 58 </help>
51 <expand macro="bunwarpj_citations" /> 59 <expand macro="bunwarpj_citations"/>
52 </tool> 60 </tool>