Mercurial > repos > imgteam > imagej2_bunwarpj_compare_elastic_raw

comparison imagej2_bunwarpj_compare_elastic_raw.xml @ 3:da91b5eaf92d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:16:58 +0000
parents 3d5f59603e13
children
comparison
equal deleted inserted replaced
2:3d5f59603e13 3:da91b5eaf92d
1 <tool id="imagej2_bunwarpj_compare_elastic_raw" name="Compare elastic and raw deformation" version="@WRAPPER_VERSION@.1"> 1 <tool id="imagej2_bunwarpj_compare_elastic_raw" name="Compare elastic and raw deformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>with ImageJ2</description> 2 <description>with ImageJ2</description>
3 <macros> 3 <macros>
4 <import>imagej2_macros.xml</import> 4 <import>imagej2_macros.xml</import>
5 </macros> 5 </macros>
6 <edam_operations> 6 <edam_operations>
13 <expand macro="fiji_requirements"/> 13 <expand macro="fiji_requirements"/>
14 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
15 #import os 15 #import os
16 #set output_log = 'output_log.txt' 16 #set output_log = 'output_log.txt'
17 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0] 17 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
18 #set source_with_ext = '.'.join([source_sans_ext, $source_image.ext]) 18 #set source_with_ext = './' + '.'.join([source_sans_ext, $source_image.ext])
19 ln -s '$source_image.file_name' '$source_with_ext' && 19 ln -s '$source_image.file_name' '$source_with_ext' &&
20 #set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0] 20 #set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
21 #set target_with_ext = '.'.join([target_sans_ext, $target_image.ext]) 21 #set target_with_ext = './' + '.'.join([target_sans_ext, $target_image.ext])
22 ln -s '$target_image.file_name' '$target_with_ext' && 22 ln -s '$target_image.file_name' '$target_with_ext' &&
23 bunwarpj -compare_elastic_raw 23 bunwarpj -compare_elastic_raw
24 '$target_with_ext' 24 '$target_with_ext'
25 '$source_with_ext' 25 '$source_with_ext'
26 '$target_elastic_transformation' 26 '$target_elastic_transformation'
27 '$source_raw_transformation' 27 '$source_raw_transformation'
28 '$output' 28 '$output'
29 &>'$output_log'; 29 2>&1 | tee '$output_log'
30 if [[ $? -ne 0 ]]; then 30 && grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output'
31 cat '$output_log' >&2;
32 else
33 grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output';
34 fi
35 ]]></command> 31 ]]></command>
36 <inputs> 32 <inputs>
37 <expand macro="param_target_image"/> 33 <expand macro="param_target_image"/>
38 <expand macro="param_source_image"/> 34 <expand macro="param_source_image"/>
39 <param format="txt" name="target_elastic_transformation" type="data" label="Elastic transformation file"/> 35 <param format="txt" name="target_elastic_transformation" type="data" label="Elastic transformation file"/>