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annotate permutate_axis.xml @ 1:64de33b5137e draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author imgteam
date Mon, 22 Jul 2019 04:58:26 -0400
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64de33b5137e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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1 <tool id="ip_permutate_axis" name="Permutate image" version="0.2">
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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2 <description>along an axis</description>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3 <requirements>
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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5 <requirement type="package" version="1.15.4">numpy</requirement>
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64de33b5137e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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6 <requirement type="package" version="0.15.1">tifffile</requirement>
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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7 </requirements>
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64de33b5137e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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8 <command detect_errors="aggressive">
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 <![CDATA[
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10 python '$__tool_directory__/permutate_axis.py' '$input' '$output' $permutate --axis $axis
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 ]]>
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64de33b5137e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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12 </command>
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d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 <inputs>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 <param name="input" type="data" format="tiff" label="Binary Image File"/>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 <param name="permutate" type="text" value="0,1,2" label="new channel order">
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 <validator type="regex" message="Input has to be a sequence of axis, separated by commas">([0-4],)+[0-4]</validator>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 </param>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 <param name="axis" type="integer" value="0" label="concatenation axis" help="Concatenation axis (0-4)" /><!-- why not have a selection from 0 to 4?-->
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 </inputs>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 <outputs>
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21 <data format="tiff" name="output"/>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 </outputs>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <tests>
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24 <test>
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25 <param name="input" value="galaxyIcon_noText.tif"/>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 </test>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 </tests>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <help>
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30 **What it does**
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 Permutates the image along a specified axis.
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 </help>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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34 <citations>
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35 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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36 </citations>
d5ab37450c44 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 </tool>