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comparison imagej2_bunwarpj_compose_raw_elastic.xml @ 3:bdc70b34153a 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 16:15:22 +0000
parents 4deffc9540a3
children
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2:4deffc9540a3 3:bdc70b34153a
1 <tool id="imagej2_bunwarpj_compose_raw_elastic" name="Compose a raw and an elastic transformation" version="@WRAPPER_VERSION@.1"> 1 <tool id="imagej2_bunwarpj_compose_raw_elastic" name="Compose a raw and an elastic transformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>into a raw transformation with bUnwarpJ</description> 2 <description>into a raw transformation with bUnwarpJ</description>
3 <macros> 3 <macros>
4 <import>imagej2_macros.xml</import> 4 <import>imagej2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="fiji_requirements"/> 6 <expand macro="fiji_requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #import os 8 #import os
9 #set output_log = 'output_log.txt' 9 #set output_log = 'output_log.txt'
10 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0] 10 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
11 #set source_with_ext = '.'.join([source_sans_ext, $source_image.ext]) 11 #set source_with_ext = './' + '.'.join([source_sans_ext, $source_image.ext])
12 ln -s '$source_image.file_name' '$source_with_ext' && 12 ln -s '$source_image.file_name' '$source_with_ext' &&
13 #set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0] 13 #set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
14 #set target_with_ext = '.'.join([target_sans_ext, $target_image.ext]) 14 #set target_with_ext = './' + '.'.join([target_sans_ext, $target_image.ext])
15 ln -s '$target_image.file_name' '$target_with_ext' && 15 ln -s '$target_image.file_name' '$target_with_ext' &&
16 bunwarpj -compose_raw_elastic 16 bunwarpj -compose_raw_elastic
17 '$target_with_ext' 17 '$target_with_ext'
18 '$source_with_ext' 18 '$source_with_ext'
19 '$target_raw_transformation' 19 '$target_raw_transformation'
20 '$source_elastic_transformation' 20 '$source_elastic_transformation'
21 '$output' 21 '$output'
22 &>'$output_log';
23 if [[ $? -ne 0 ]]; then
24 cat '$output_log' >&2;
25 fi
26 ]]></command> 22 ]]></command>
27 <inputs> 23 <inputs>
28 <expand macro="param_target_image"/> 24 <expand macro="param_target_image"/>
29 <expand macro="param_source_image"/> 25 <expand macro="param_source_image"/>
30 <param format="txt" name="target_raw_transformation" type="data" label="Target inverse transformation"/> 26 <param format="txt" name="target_raw_transformation" type="data" label="Target inverse transformation"/>