comparison imagej2_bunwarpj_align.xml @ 3:711adedc5bb8 draft default tip

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

2:0a0d2dfd17e0

<tool id="imagej2_bunwarpj_align" name="Align two images" version="@WRAPPER_VERSION@.1">
    <description>with ImageJ2</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <edam_operations>

## ImageJ2 requires file extensions to be valid image data types.
#set source_out_suffix = '.' + str($source_out_datatype)
#set target_out_suffix = '.' + str($target_out_datatype)
#set source_image_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
#set source_image_with_ext = '.'.join([$source_image_sans_ext, $source_image.ext])
ln -s '$source_image.file_name' '$source_image_with_ext';
#set target_image_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
#set target_image_with_ext = '.'.join([$target_image_sans_ext, $target_image.ext])
ln -s '$target_image.file_name' '$target_image_with_ext';

#set save_transformation = str($advanced_options_cond.advanced_options) == 'save_transformation'
#set mono = str($advanced_options_cond.advanced_options) == 'mono'
#set landmarks = str($advanced_options_cond.advanced_options) == 'landmarks'
#set affine = str($advanced_options_cond.advanced_options) == 'affine'

#if str($align_with_mask_cond.align_with_mask) == 'yes':
    #set source_mask_sans_ext = $os.path.splitext($os.path.basename($align_with_mask_cond.source_mask.file_name))[0]
    #set source_mask_with_ext = '.'.join([$source_mask_sans_ext, $source_mask.ext])
    #set source_mask = $source_mask_with_ext
    ln -s '$align_with_mask_cond.source_mask.file_name' '$source_mask_with_ext';
    #set target_mask_sans_ext = $os.path.splitext($os.path.basename($align_with_mask_cond.target_mask.file_name))[0]
    #set target_mask_with_ext = '.'.join([$target_mask_sans_ext, $target_mask.ext])
    #set target_mask = $target_mask_with_ext
    ln -s '$align_with_mask_cond.target_mask.file_name' '$target_mask_with_ext';
#else:
    #set source_mask = 'NULL'
    #set target_mask = 'NULL'

#set tmp_source_out_transf_name_sans_ext = $os.path.splitext($source_out.file_name)[0]
#set tmp_source_out_transf_name = $tmp_source_out_transf_name_sans_ext + '_transf.txt'
touch '$tmp_source_out_transf_name';

## Align the two images using bUnwarpJ.
bunwarpj -align
'$target_image_with_ext'
'$target_mask'
'$source_image_with_ext'
'$source_mask'
$min_scale_def

    '-mono'
#end if
#if $save_transformation:
    '-save_transformation'
#end if
&>'$error_log';
#if $save_transformation:
    mv '$tmp_source_out_transf_name' '$source_trans_out';
    mv '$tmp_target_out_transf_name' '$target_trans_out';
#end if
if [[ $? -ne 0 ]]; then
    cat '$error_log' >&2;
fi
]]></command>
    <inputs>
        <expand macro="param_target_image"/>
        <expand macro="param_source_image"/>
        <conditional name="align_with_mask_cond">

        <data format="txt" name="target_trans_out" label="${tool.name} (target transf matrix) ${on_string}">
            <filter>advanced_options_cond['advanced_options'] == "save_transformation"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <!-- Align two images without landmarks or mask and not saving transformation matrices -->
            <expand macro="test_target_source_images"/>
            <param name="max_subsamp_fact" value="1"/>
            <output name="source_out" file="registered_source1.png" compare="sim_size"/>
            <output name="target_out" file="registered_target1.png" compare="sim_size"/>
        </test>
        <test>
            <!-- Align two images without landmarks or mask, but saving transformation matrices -->
            <expand macro="test_target_source_images"/>
            <param name="max_subsamp_fact" value="1"/>
            <param name="advanced_options" value="save_transformation"/>
            <output name="source_out" file="registered_source1.png" compare="sim_size"/>
            <output name="target_out" file="registered_target1.png" compare="sim_size"/>
            <output name="source_trans_out" file="source_elastic_transformation_out.txt" compare="contains"/>
            <output name="target_trans_out" file="target_elastic_transformation_out.txt" compare="contains"/>
        </test>
        <test>
            <!-- Align two images without landmarks but with mask, not saving transformation matrices -->
            <expand macro="test_target_source_images"/>
            <param name="align_with_mask" value="yes"/>
            <param name="target_mask" value="mask_white.png"/>
            <param name="source_mask" value="mask_ramp.gif"/>
            <param name="max_subsamp_fact" value="1"/>
            <output name="source_out" file="registered_source2.png" compare="sim_size"/>
            <output name="target_out" file="registered_target2.png" compare="sim_size"/>
        </test>
    </tests>
    <help>
**What it does**

3:711adedc5bb8

<tool id="imagej2_bunwarpj_align" name="Align two images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <description>with ImageJ2</description>
    <macros>
        <import>imagej2_macros.xml</import>
    </macros>
    <edam_operations>

## ImageJ2 requires file extensions to be valid image data types.
#set source_out_suffix = '.' + str($source_out_datatype)
#set target_out_suffix = '.' + str($target_out_datatype)
#set source_image_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
#set source_image_with_ext = './' + '.'.join([$source_image_sans_ext, $source_image.ext])
ln -s '$source_image.file_name' '$source_image_with_ext';
#set target_image_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
#set target_image_with_ext = './' + '.'.join([$target_image_sans_ext, $target_image.ext])
ln -s '$target_image.file_name' '$target_image_with_ext';

#set save_transformation = str($advanced_options_cond.advanced_options) == 'save_transformation'
#set mono = str($advanced_options_cond.advanced_options) == 'mono'
#set landmarks = str($advanced_options_cond.advanced_options) == 'landmarks'
#set affine = str($advanced_options_cond.advanced_options) == 'affine'

#if str($align_with_mask_cond.align_with_mask) == 'yes':
    #set source_mask_sans_ext = $os.path.splitext($os.path.basename($align_with_mask_cond.source_mask.file_name))[0]
    #set source_mask_with_ext =  './' + '.'.join([$source_mask_sans_ext, $source_mask.ext])
    #set source_mask = $source_mask_with_ext
    ln -s '$align_with_mask_cond.source_mask.file_name' '$source_mask_with_ext';
    #set target_mask_sans_ext = $os.path.splitext($os.path.basename($align_with_mask_cond.target_mask.file_name))[0]
    #set target_mask_with_ext =  './' + '.'.join([$target_mask_sans_ext, $target_mask.ext])
    #set target_mask = $target_mask_with_ext
    ln -s '$align_with_mask_cond.target_mask.file_name' '$target_mask_with_ext';
#else:
    #set source_mask = 'NULL'
    #set target_mask = 'NULL'

#set tmp_source_out_transf_name_sans_ext = $os.path.splitext($source_out.file_name)[0]
#set tmp_source_out_transf_name = $tmp_source_out_transf_name_sans_ext + '_transf.txt'
touch '$tmp_source_out_transf_name';

## Align the two images using bUnwarpJ.
## The option -XX:ActiveProcessorCount="1" was set in version 20231211 to ensure reproducibility
bunwarpj -XX:ActiveProcessorCount="1" -align
'$target_image_with_ext'
'$target_mask'
'$source_image_with_ext'
'$source_mask'
$min_scale_def

    '-mono'
#end if
#if $save_transformation:
    '-save_transformation'
#end if
#if $save_transformation:
    && mv '$tmp_source_out_transf_name' '$source_trans_out'
    && mv '$tmp_target_out_transf_name' '$target_trans_out';
#end if
]]></command>
    <inputs>
        <expand macro="param_target_image"/>
        <expand macro="param_source_image"/>
        <conditional name="align_with_mask_cond">

        <data format="txt" name="target_trans_out" label="${tool.name} (target transf matrix) ${on_string}">
            <filter>advanced_options_cond['advanced_options'] == "save_transformation"</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <!-- Align two images without landmarks or mask and not saving transformation matrices -->
            <expand macro="test_target_source_images"/>
            <param name="max_subsamp_fact" value="1"/>
            <output name="source_out" file="registered_source1_forced1cpu.png" compare="image_diff"/>
            <output name="target_out" file="registered_target1_forced1cpu.png" compare="image_diff"/>
        </test>
        <test expect_num_outputs="4">
            <!-- Align two images without landmarks or mask, but saving transformation matrices -->
            <expand macro="test_target_source_images"/>
            <param name="max_subsamp_fact" value="1"/>
            <param name="advanced_options" value="save_transformation"/>
            <output name="source_out" file="registered_source1_forced1cpu.png" compare="image_diff"/>
            <output name="target_out" file="registered_target1_forced1cpu.png" compare="image_diff"/>
            <output name="source_trans_out" file="source_elastic_transformation_out.txt" compare="contains"/>
            <output name="target_trans_out" file="target_elastic_transformation_out.txt" compare="contains"/>
        </test>
        <test expect_num_outputs="2">
            <!-- Align two images without landmarks but with mask, not saving transformation matrices -->
            <expand macro="test_target_source_images"/>
            <param name="align_with_mask" value="yes"/>
            <param name="target_mask" value="mask_white.png"/>
            <param name="source_mask" value="mask_ramp.gif"/>
            <param name="max_subsamp_fact" value="1"/>
            <output name="source_out" file="registered_source2_forced1cpu.png" compare="image_diff"/>
            <output name="target_out" file="registered_target2_forced1cpu.png" compare="image_diff"/>
        </test>
    </tests>
    <help>
**What it does**