comparison imagej2_bunwarpj_compare_raw.xml @ 3:b0da913f048e draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56

2:77411a986a70

<tool id="imagej2_bunwarpj_compare_raw" name="Compare two raw deformations" version="@WRAPPER_VERSION@.1">
    <description>with ImageJ2</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <edam_operations>

    <expand macro="fiji_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#import os
#set output_log = 'output_log.txt'
#set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
#set source_with_ext = '.'.join([source_sans_ext, $source_image.ext])
ln -s '$source_image.file_name' '$source_with_ext' &&
#set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
#set target_with_ext = '.'.join([target_sans_ext, $target_image.ext])
ln -s '$target_image.file_name' '$target_with_ext' &&
bunwarpj -compare_raw
'$target_with_ext'
'$source_with_ext'
'$target_raw_transformation'
'$source_raw_transformation'
&>'$output_log';
if [[ $? -ne 0 ]]; then
    cat '$output_log' >&2;
else
    grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output';
fi
]]></command>
    <inputs>
        <expand macro="param_target_image"/>
        <expand macro="param_source_image"/>
        <param format="txt" name="target_raw_transformation" type="data" label="Raw transformation file 1"/>

3:b0da913f048e

<tool id="imagej2_bunwarpj_compare_raw" name="Compare two raw deformations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <description>with ImageJ2</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <edam_operations>

    <expand macro="fiji_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#import os
#set output_log = 'output_log.txt'
#set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
#set source_with_ext = './' + '.'.join([source_sans_ext, $source_image.ext])
ln -s '$source_image.file_name' '$source_with_ext' &&
#set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
#set target_with_ext = './' + '.'.join([target_sans_ext, $target_image.ext])
ln -s '$target_image.file_name' '$target_with_ext' &&
bunwarpj -compare_raw
'$target_with_ext'
'$source_with_ext'
'$target_raw_transformation'
'$source_raw_transformation'
2>&1 | tee '$output_log'
&& grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output'
]]></command>
    <inputs>
        <expand macro="param_target_image"/>
        <expand macro="param_source_image"/>
        <param format="txt" name="target_raw_transformation" type="data" label="Raw transformation file 1"/>