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comparison imagej2_bunwarpj_compare_raw.xml @ 3:b0da913f048e draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 15:59:18 +0000
parents 77411a986a70
children
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2:77411a986a70 3:b0da913f048e
1 <tool id="imagej2_bunwarpj_compare_raw" name="Compare two raw deformations" version="@WRAPPER_VERSION@.1"> 1 <tool id="imagej2_bunwarpj_compare_raw" name="Compare two raw deformations" 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' '$target_with_ext' &&
23 bunwarpj -compare_raw 23 bunwarpj -compare_raw
24 '$target_with_ext' 24 '$target_with_ext'
25 '$source_with_ext' 25 '$source_with_ext'
26 '$target_raw_transformation' 26 '$target_raw_transformation'
27 '$source_raw_transformation' 27 '$source_raw_transformation'
28 &>'$output_log'; 28 2>&1 | tee '$output_log'
29 if [[ $? -ne 0 ]]; then 29 && grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output'
30 cat '$output_log' >&2;
31 else
32 grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output';
33 fi
34 ]]></command> 30 ]]></command>
35 <inputs> 31 <inputs>
36 <expand macro="param_target_image"/> 32 <expand macro="param_target_image"/>
37 <expand macro="param_source_image"/> 33 <expand macro="param_source_image"/>
38 <param format="txt" name="target_raw_transformation" type="data" label="Raw transformation file 1"/> 34 <param format="txt" name="target_raw_transformation" type="data" label="Raw transformation file 1"/>