annotate imagej2_bunwarpj_compare_raw.xml @ 2:77411a986a70 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

<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>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <xrefs>
        <xref type="bio.tools">imagej</xref>
        <xref type="biii">imagej2</xref>
    </xrefs>
    <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"/>
        <param format="txt" name="source_raw_transformation" type="data" label="Raw transformation file 2"/>
    </inputs>
    <outputs>
        <data name="output" format="txt" label="${tool.name} (same direction) on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <expand macro="test_bunwarpj_raw_transform"/>
            <output name="output" file="warping_index1.txt" compare="contains"/>
        </test>
        <test>
            <expand macro="test_target_source_images"/>
            <param name="target_raw_transformation" value="source_raw_transformation.txt"/>
            <param name="source_raw_transformation" value="source_raw_transformation.txt"/>
            <output name="output" file="warping_index2.txt"/>
        </test>
    </tests>
    <help>
**What it does**

<![CDATA[
Calculates the warping index of two raw transformations (same direction). The transformation
files must be in "raw" format, which is the same format as the files created with the
**Convert elastic transformation to raw** tool.

]]>

    </help>
    <expand macro="bunwarpj_citations"/>
</tool>