Mercurial > repos > imgteam > slice_image
comparison slice_image.xml @ 0:aacfbd7c4af6 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
| author | imgteam |
|---|---|
| date | Sat, 09 Feb 2019 14:46:50 -0500 |
| parents | |
| children | 8856a7c85e4c |
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| -1:000000000000 | 0:aacfbd7c4af6 |
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| 1 <tool id="ip_slice_image" name="Slice Image" version="0.2"> | |
| 2 <description>into smaller patches</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.14.2">scikit-image</requirement> | |
| 5 <requirement type="package" version="1.15.4">numpy</requirement> | |
| 6 <!-- <requirement type="package" version="1.1.0">scipy</requirement> --> | |
| 7 </requirements> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 mkdir ./out && | |
| 11 python '$__tool_directory__/slice_image.py' | |
| 12 '$input_file' ./out | |
| 13 --stride $stride --window_size $patch_size --bg_thresh $bg_thresh | |
| 14 --limit_slices $limit_slices | |
| 15 #if $limit_slices: | |
| 16 --n_thresh $n_thresh | |
| 17 #end if | |
| 18 #if $control_rng: | |
| 19 --seed $seed | |
| 20 #end if | |
| 21 && ls -l ./out | |
| 22 ]]> | |
| 23 </command> | |
| 24 <inputs> | |
| 25 <param name="input_file" type="data" format="tiff,png,jpg,bmp" label="Input image"/> | |
| 26 <!--<param name="out_folder" type="text" label="Output folder for image slices"/> | |
| 27 <param name="label_file" type="data" format="tiff,png,jpg,bmp" label="Auxiliary label file to split in the same way"/>--> | |
| 28 <param name="stride" type="integer" optional="true" value="16"/> | |
| 29 <param name="patch_size" type="integer" optional="true" value="64" label="Size of resulting (quadratic-shaped) slices"/> | |
| 30 <param name="bg_thresh" type="float" optional="true" value="0" label="Threshold to not be considered background"/> | |
| 31 <param name="limit_slices" type="boolean" checked="true" label="Should the number of slices be limited?"/> | |
| 32 <param name="n_thresh" type="integer" optional="true" label="Maximum amount of slices; only needed if limit_slices is selected"/> | |
| 33 <param name="control_rng" type="boolean" checked="false" label="Boolean that controls if a certain seed should be selected for the random number generator"/> | |
| 34 <param name="seed" type="integer" value="1" | |
| 35 label="Seed chosen for the random number generator of the random choice of limited slices. Only required if cotrol_rng is selected"/> | |
| 36 </inputs> | |
| 37 <outputs> | |
| 38 <collection name="slices" type="list" label="Slices obtained from input"> | |
| 39 <discover_datasets directory="out" format="tiff" pattern="__name__"/> | |
| 40 </collection> | |
| 41 </outputs> | |
| 42 <tests> | |
| 43 <test> | |
| 44 <param name="input_file" value="input.tiff"/> | |
| 45 <param name="limit_slices" value="true"/> | |
| 46 <param name="n_thresh" value="5"/> | |
| 47 <param name="control_rng" value="true"/> | |
| 48 <param name="seed" value="17"/> | |
| 49 <output_collection name="slices" type="list"> | |
| 50 <element name="148.tiff" file="input_148.tiff" ftype="tiff" compare="sim_size"/> | |
| 51 <element name="155.tiff" file="input_155.tiff" ftype="tiff" compare="sim_size"/> | |
| 52 <element name="187.tiff" file="input_187.tiff" ftype="tiff" compare="sim_size"/> | |
| 53 <element name="212.tiff" file="input_212.tiff" ftype="tiff" compare="sim_size"/> | |
| 54 <element name="267.tiff" file="input_267.tiff" ftype="tiff" compare="sim_size"/> | |
| 55 </output_collection> | |
| 56 </test> | |
| 57 </tests> | |
| 58 <help> | |
| 59 **What it does** | |
| 60 | |
| 61 Slices image into multiple smaller patches. | |
| 62 </help> | |
| 63 <citations> | |
| 64 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> | |
| 65 </citations> | |
| 66 </tool> |