comparison basic_illumination.xml @ 1:db20f09300bd draft

planemo upload for repository https://github.com/labsyspharm/basic-illumination commit d62977a02ee6e0e5100479d6d7b19eb4a8cf9761

0:fd8dfd64f25e

<tool id="basic_illumination" name="BaSiC Illumination" version="@VERSION@.3" profile="17.09">
    <description>ImageJ BaSiC shading correction for use with Ashlar</description>
    <macros>
        <import>macros.xml</import>
    </macros>
 
    <expand macro="requirements"/>
    @VERSION_CMD@

    <command detect_errors="exit_code"><![CDATA[
    ln -s $in_files "${in_files.name}" &&

    #set $outname = str($in_files.name).replace('.ome.tiff','')

    @CMD_BEGIN@

    "filename='${in_files.name}',output_dir='.',experiment_name='output'";

   <outputs>
       <data format="tiff" name="output_dfp" label="${tool.name} on ${on_string}: DFP" from_work_dir="output-dfp.tif"/>
       <data format="tiff" name="output_ffp" label="${tool.name} on ${on_string}: FFP" from_work_dir="output-ffp.tif"/>
    </outputs>

    <help><![CDATA[
basic-illumination
ImageJ BaSiC shading correction for use with Ashlar

Running as a Docker container
Create a container:

docker run -it -v /path/to/data:/data labsyspharm/basic-illumination bash
(where /path/to/data is the data directory on your local machine. Your data will be mapped to /data inside the container)

Once inside the container, do ls /data to ensure your data is there, followed by

ImageJ-linux64 --ij2 --headless --run imagej_basic_ashlar.py \
  "filename='/data/input.ome.tiff',output_dir='/data/',experiment_name='my_experiment'"
for each input.ome.tiff in your data directory.

OHSU Wrapper Repo: https://github.com/ohsu-comp-bio/basic-illumination
Conda Package Available From: https://anaconda.org/ohsu-comp-bio/basic-illumination
    ]]></help>
    <expand macro="citations" />
</tool>

1:db20f09300bd

<tool id="basic_illumination" name="BaSiC Illumination" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>ImageJ BaSiC shading correction for use with Ashlar</description>
    <macros>
        <import>macros.xml</import>
    </macros>
 
    <expand macro="requirements"/>
    <expand macro="version_cmd"/>

    <command detect_errors="exit_code"><![CDATA[
    ln -s '$in_files' '${in_files.name}' &&

    #set $outname = str('$in_files.name').replace('.ome.tiff','')

    @CMD_BEGIN@

    "filename='${in_files.name}',output_dir='.',experiment_name='output'";

   <outputs>
       <data format="tiff" name="output_dfp" label="${tool.name} on ${on_string}: DFP" from_work_dir="output-dfp.tif"/>
       <data format="tiff" name="output_ffp" label="${tool.name} on ${on_string}: FFP" from_work_dir="output-ffp.tif"/>
    </outputs>
    <tests>
        <test>
            <param name="in_files" value="test.tiff" />
            <output name="output_dfp" ftype="tiff">
                <assert_contents>
                    <has_size value="350000" delta="50000" />
                </assert_contents>
            </output>
            <output name="output_ffp" ftype="tiff">
                <assert_contents>
                    <has_size value="350000" delta="50000" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
-------------------        
basic-illumination
-------------------

**ImageJ BaSiC shading correction for use with Ashlar**
**basic-illumination** can read image data directly from BioFormats-supported microscope
vendor file formats as well as a directory of plain TIFF files. Output includes a flat field and
dark field image per input file.
    ]]></help>
    <expand macro="citations" />
</tool>