Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw
comparison imagej2_bunwarpj_convert_to_raw.xml @ 1:7f9840d3b7e7 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 16:48:49 +0000 |
parents | 95fb6fa70c2f |
children | 0cdd96322600 |
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0:95fb6fa70c2f | 1:7f9840d3b7e7 |
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1 <?xml version='1.0' encoding='UTF-8'?> | |
2 <tool id="imagej2_bunwarpj_convert_to_raw" name="Convert elastic transformation to raw" version="@WRAPPER_VERSION@.0"> | 1 <tool id="imagej2_bunwarpj_convert_to_raw" name="Convert elastic transformation to raw" version="@WRAPPER_VERSION@.0"> |
3 <description>with bUnwarpJ</description> | 2 <description>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 $__tool_directory__/imagej2_bunwarpj_convert_to_raw.py | 9 #set output_log = 'output_log.txt' |
11 --target_image "$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($target_image.file_name))[0] |
15 --elastic_transformation "$elastic_transformation" | 14 #set target_with_ext = '.'.join([target_sans_ext, $target_image.ext]) |
16 --raw_transformation "$raw_transformation" | 15 ln -s '$target_image.file_name' '$target_with_ext' && |
17 ]]> | 16 bunwarpj -convert_to_raw |
18 </command> | 17 '$target_with_ext' |
18 '$source_with_ext' | |
19 '$elastic_transformation' | |
20 '$raw_transformation' | |
21 &>'$output_log'; | |
22 if [[ $? -ne 0 ]]; then | |
23 cat '$output_log' >&2; | |
24 fi | |
25 ]]></command> | |
19 <inputs> | 26 <inputs> |
20 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/> | 27 <expand macro="param_target_image"/> |
21 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/> | 28 <expand macro="param_source_image"/> |
22 <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy --> | 29 <!-- Support for a bUnwarpJ elastic transformation datatype should be added to Galaxy --> |
23 <param format="txt" name="elastic_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in elastic format"/> | 30 <param format="txt" name="elastic_transformation" type="data" label="Elastic transformation" help="As saved by bUnwarpJ in elastic format"/> |
24 </inputs> | 31 </inputs> |
25 <outputs> | 32 <outputs> |
26 <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy --> | 33 <!-- Support for a bUnwarpJ raw transformation datatype should be added to Galaxy --> |
27 <data name="raw_transformation" format="txt" label="${tool.name} on ${on_string}: Raw transformation" /> | 34 <data name="raw_transformation" format="txt"/> |
28 </outputs> | 35 </outputs> |
29 <tests> | 36 <tests> |
30 <test> | 37 <test> |
31 <param name="target_image" value="dotblot.jpg" /> | 38 <expand macro="test_target_source_images"/> |
32 <param name="source_image" value="blobs.gif" /> | 39 <param name="elastic_transformation" value="source_elastic_transformation.txt" ftype="txt"/> |
33 <param name="elastic_transformation" value="source_elastic_transformation.txt" ftype="txt" /> | 40 <output name="raw_transformation" file="source_raw_transformation.txt" ftype="txt"/> |
34 <output name="raw_transformation" file="source_raw_transformation.txt" ftype="txt" /> | |
35 </test> | 41 </test> |
36 </tests> | 42 </tests> |
37 <help> | 43 <help> |
38 **What it does** | 44 **What it does** |
39 | 45 |
43 option in the **Align two images with bUnwarpJ** tool. | 49 option in the **Align two images with bUnwarpJ** tool. |
44 | 50 |
45 ]]> | 51 ]]> |
46 | 52 |
47 </help> | 53 </help> |
48 <expand macro="bunwarpj_citations" /> | 54 <expand macro="bunwarpj_citations"/> |
49 </tool> | 55 </tool> |