view imagej2_bunwarpj_compare_elastic_raw.xml @ 1:2be338fc671e draft default tip

"planemo upload for repository commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:44:56 +0000
parents 1bffabc15695
line wrap: on
line source

<tool id="imagej2_bunwarpj_compare_elastic_raw" name="Compare elastic and raw deformation" version="@WRAPPER_VERSION@.0">
    <description>by warping index with bUnwarpJ</description>
    <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_elastic_raw
if [[ $? -ne 0 ]]; then
    cat '$output_log' >&2;
    grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output';
        <expand macro="param_target_image"/>
        <expand macro="param_source_image"/>
        <param format="txt" name="target_elastic_transformation" type="data" label="Elastic transformation file"/>
        <param format="txt" name="source_raw_transformation" type="data" label="Raw transformation file"/>
        <data name="output" format="txt" label="${} (same direction) on ${on_string}"/>
            <expand macro="test_target_source_images"/>
            <param name="target_elastic_transformation" value="target_elastic_transformation.txt"/>
            <param name="source_raw_transformation" value="source_raw_transformation.txt"/>
            <output name="output" file="warping_index_raw.txt" compare="contains"/>
**What it does**

Calculates the warping index of an elastic transformation and a raw transformation. The elastic
transformation file must be in the same format as the files created with the **Save transformation**
option of the **Align two images with bUnwarpJ** tool, while the raw transformation file must be
in the same format as the file produced by the **Convert elastic transformation to raw with bUnwarpJ**


    <expand macro="bunwarpj_citations"/>