comparison bf2raw.xml @ 2:51d1460d03e6 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit d12bb8de65b311ab1c07b69147388a4bd3d9887a

1:21fedce225f6

<tool id="bf2raw" name="Convert to OME-Zarr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0">
    <description>with Bio-Formats</description>
    <macros>
        <import>creators.xml</import>
        <token name="@TOOL_VERSION@">0.7.0</token>
        <token name="@VERSION_SUFFIX@">4</token>
    </macros>
    <creator>
        <expand macro="creators/bugraoezdemir"/>
        <expand macro="creators/bmcv"/>
        <expand macro="creators/kostrykin"/>

    <requirements>
        <container type="docker">quay.io/biocontainers/mulled-v2-ea5a9ffc5f22f92a78f0cd24aac43eb503c0e523:4c010c399f61cde74da64343581999ada3e11e24-0</container>
    </requirements>
    <command><![CDATA[

if [ ! -d $output.files_path ]; then
    mkdir -p $output.files_path;
fi;

ln -s ${io_options.input} ./input;

export _JAVA_OPTIONS="-Djava.io.tmpdir=/usr/local/man/" && bioformats2raw ./input $output.files_path
#if $bf2raw_params.multiscales['options'] == 'auto':
    --target-min-size $bf2raw_params.multiscales.min_xy_size
#elif $bf2raw_params.multiscales['options'] == 'manual':
    --resolutions $bf2raw_params.resolutions
#end if

#if not str($bf2raw_params.dimension_order) == 'keep input order':
    --dimension-order $bf2raw_params.dimension_order
#end if
--overwrite &> /dev/null;

#if str($io_options.subgroup) != ''
    mv ${output.files_path}/${io_options.subgroup} ./subdir;
    mv ${output.files_path}/OME ./subdir/OME;
    rm -rf ${output.files_path};
    mv ./subdir ${output.files_path};
#end if

    ]]></command>
    <inputs>
        <section name="io_options" title="Input/Output" expanded="true">
            <param name="input" type="data"
                   format="scn,ndpi,tf8,vms,xml,pcx,binary,hdr,mov,psd,pbm,nrrd,tiff,pgm,ppm,txt,tf2,zip,top,gif,wav,btf,bmp,png,gz,cif,fli,btf,jpg,avi,html,sif,csv,ome.tiff,par,fits,jp2,eps,nhdr,svs,mrc"
                   label="Input image"/>
            <param name="subgroup" type="text" value="" optional="true" label="Select a subgroup"
                   help='Only export a subgroup of the Zarr dataset (e.g., use "&lt;tt&gt;0&lt;/tt&gt;" to only export the &lt;tt&gt;/0&lt;/tt&gt; subgroup of the Zarr). Leave empty to export the full Zarr.'/>
        </section>
        <section name="bf2raw_params" title="Parameters fed to file conversion module">
            <conditional name="multiscales" >
                <param name="options" type="select" multiple="false" label="How should the number of resolutions be determined?" >
                    <option value="auto" selected="true">auto</option>

2:51d1460d03e6

<tool id="bf2raw" name="Convert to OME-Zarr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0">
    <description>with Bio-Formats</description>
    <macros>
        <import>creators.xml</import>
        <token name="@TOOL_VERSION@">0.7.0</token>
        <token name="@VERSION_SUFFIX@">5</token>
    </macros>
    <creator>
        <expand macro="creators/bugraoezdemir"/>
        <expand macro="creators/bmcv"/>
        <expand macro="creators/kostrykin"/>

    <requirements>
        <container type="docker">quay.io/biocontainers/mulled-v2-ea5a9ffc5f22f92a78f0cd24aac43eb503c0e523:4c010c399f61cde74da64343581999ada3e11e24-0</container>
    </requirements>
    <command><![CDATA[

## Create final output directory
if [ ! -d $output.files_path ]; then
    mkdir -p $output.files_path;
fi;

## Use an intermediate output directory if only a subgroup of the Zarr is wanted for export
#if str($io_options.subgroup) == ''
    ln -s $output.files_path ./output;
#else
    mkdir ./output;
#end if

## Input symlink to obscure the dataset directory for reproducible results
ln -s ${io_options.input} ./input;

export _JAVA_OPTIONS="-Djava.io.tmpdir=/usr/local/man/" && bioformats2raw ./input ./output/.
#if $bf2raw_params.multiscales['options'] == 'auto':
    --target-min-size $bf2raw_params.multiscales.min_xy_size
#elif $bf2raw_params.multiscales['options'] == 'manual':
    --resolutions $bf2raw_params.resolutions
#end if

#if not str($bf2raw_params.dimension_order) == 'keep input order':
    --dimension-order $bf2raw_params.dimension_order
#end if
--overwrite &> /dev/null;

## Optionally, export a subgroup of the Zarr
#if str($io_options.subgroup) != ''
    mv "./output/${io_options.subgroup}"/* "./output/${io_options.subgroup}"/.* "${output.files_path}/";
    mv "./output/OME" "${output.files_path}/OME";
#end if

    ]]></command>
    <inputs>
        <section name="io_options" title="Input/Output" expanded="true">
            <param name="input" type="data"
                   format="scn,ndpi,tf8,vms,xml,pcx,binary,hdr,mov,psd,pbm,nrrd,tiff,pgm,ppm,txt,tf2,zip,top,gif,wav,btf,bmp,png,gz,cif,fli,btf,jpg,avi,html,sif,csv,ome.tiff,par,fits,jp2,eps,nhdr,svs,mrc"
                   label="Input image"/>
            <param name="subgroup" type="text" value="" optional="true" label="Select a subgroup"
                   help='Only export a subgroup of the Zarr dataset (e.g., use "&lt;tt&gt;0&lt;/tt&gt;" to only export the &lt;tt&gt;/0&lt;/tt&gt; subgroup of the Zarr). Leave empty to export the full Zarr.'>
                <validator type="regex" message="Subgroup name cannot be empty." negate="true">.*//.*</validator>
                <validator type="expression" message='Subgroup name must not start with a "/"' negate="true">value.startswith("/")</validator>
                <validator type="expression" message='Subgroup name must not end with a "/"' negate="true">value.endswith("/")</validator>
            </param>
        </section>
        <section name="bf2raw_params" title="Parameters fed to file conversion module">
            <conditional name="multiscales" >
                <param name="options" type="select" multiple="false" label="How should the number of resolutions be determined?" >
                    <option value="auto" selected="true">auto</option>