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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
author thomaswollmann
date Wed, 12 Dec 2018 04:50:51 -0500
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8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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1 <tool id="permutate_axis" name="Permutate Axis" version="0.1">
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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2 <description> Permutates axes </description>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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3 <requirements>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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4 <requirement type="package" version="0.14.0">scikit-image</requirement>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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5 <requirement type="package" version="1.15.4">numpy</requirement>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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6 </requirements>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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7 <command>
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8 <![CDATA[
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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9 python '$__tool_directory__/permutate_axis.py' '$input' '$output' $permutate --axis $axis
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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10 ]]>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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11 </command>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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12 <inputs>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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13 <param name="input" type="data" format="tiff" label="Binary Image File"/>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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14 <param name="permutate" type="text" value="0,1,2" label="new channel order">
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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15 <validator type="regex" message="Input has to be a sequence of axis, separated by commas">([0-4],)+[0-4]</validator>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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16 </param>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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17 <param name="axis" type="integer" value="0" label="concatenation axis" help="Concatenation axis (0-4)" /><!-- why not have a selection from 0 to 4?-->
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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18 </inputs>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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19 <outputs>
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20 <data format="tiff" name="output"/>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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21 </outputs>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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22 <tests>
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23 <test>
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24 <param name="input" value="galaxyIcon_noText.tif"/>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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25 <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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26 </test>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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27 </tests>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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28 <help>Permutates the image along a specified axis.</help>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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29 <citations>
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30 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
8fb82d514666 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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31 </citations>
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32 </tool>