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annotate slice_image.xml @ 1:8856a7c85e4c draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:03:25 -0500
parents aacfbd7c4af6
children f312d414f234
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8856a7c85e4c "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
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1 <tool id="ip_slice_image" name="Slice Image" version="0.3">
0
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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2 <description>into smaller patches</description>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3 <requirements>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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5 <requirement type="package" version="1.15.4">numpy</requirement>
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8856a7c85e4c "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
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6 <requirement type="package" version="1.1.0">scipy</requirement>
8856a7c85e4c "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
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7 <requirement type="package" version="0.15.1">tifffile</requirement>
0
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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8 </requirements>
1
8856a7c85e4c "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
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9 <command detect_errors="aggressive">
0
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10 <![CDATA[
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 mkdir ./out &&
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 python '$__tool_directory__/slice_image.py'
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 '$input_file' ./out
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 --stride $stride --window_size $patch_size --bg_thresh $bg_thresh
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 --limit_slices $limit_slices
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 #if $limit_slices:
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 --n_thresh $n_thresh
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 #end if
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 #if $control_rng:
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 --seed $seed
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 #end if
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 && ls -l ./out
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 ]]>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 </command>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 <inputs>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <param name="input_file" type="data" format="tiff,png,jpg,bmp" label="Input image"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 <!--<param name="out_folder" type="text" label="Output folder for image slices"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 <param name="label_file" type="data" format="tiff,png,jpg,bmp" label="Auxiliary label file to split in the same way"/>-->
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <param name="stride" type="integer" optional="true" value="16"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 <param name="patch_size" type="integer" optional="true" value="64" label="Size of resulting (quadratic-shaped) slices"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 <param name="bg_thresh" type="float" optional="true" value="0" label="Threshold to not be considered background"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 <param name="limit_slices" type="boolean" checked="true" label="Should the number of slices be limited?"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 <param name="n_thresh" type="integer" optional="true" label="Maximum amount of slices; only needed if limit_slices is selected"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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34 <param name="control_rng" type="boolean" checked="false" label="Boolean that controls if a certain seed should be selected for the random number generator"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 <param name="seed" type="integer" value="1"
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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36 label="Seed chosen for the random number generator of the random choice of limited slices. Only required if cotrol_rng is selected"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 </inputs>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 <outputs>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 <collection name="slices" type="list" label="Slices obtained from input">
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40 <discover_datasets directory="out" format="tiff" pattern="__name__"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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41 </collection>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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42 </outputs>
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43 <tests>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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44 <test>
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45 <param name="input_file" value="input.tiff"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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46 <param name="limit_slices" value="true"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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47 <param name="n_thresh" value="5"/>
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48 <param name="control_rng" value="true"/>
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49 <param name="seed" value="17"/>
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50 <output_collection name="slices" type="list">
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51 <element name="148.tiff" file="input_148.tiff" ftype="tiff" compare="sim_size"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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52 <element name="155.tiff" file="input_155.tiff" ftype="tiff" compare="sim_size"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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53 <element name="187.tiff" file="input_187.tiff" ftype="tiff" compare="sim_size"/>
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54 <element name="212.tiff" file="input_212.tiff" ftype="tiff" compare="sim_size"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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55 <element name="267.tiff" file="input_267.tiff" ftype="tiff" compare="sim_size"/>
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56 </output_collection>
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57 </test>
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58 </tests>
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59 <help>
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60 **What it does**
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61
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62 Slices image into multiple smaller patches.
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63 </help>
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64 <citations>
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65 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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66 </citations>
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67 </tool>