Mercurial > repos > imgteam > imagej2_bunwarpj_compare_elastic_raw
comparison imagej2_bunwarpj_compare_elastic_raw.xml @ 1:2be338fc671e draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
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date | Mon, 28 Sep 2020 16:44:56 +0000 |
parents | 1bffabc15695 |
children | 3d5f59603e13 |
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0:1bffabc15695 | 1:2be338fc671e |
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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> |