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annotate permutate_axis.xml @ 2:91e255c78eb5 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:02:53 -0500
parents 5b82f2186244
children 7e7215e721af
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5b82f2186244 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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0bbe34198e24 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>
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3 <requirements>
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
0bbe34198e24 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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5b82f2186244 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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0bbe34198e24 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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5b82f2186244 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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8 <command detect_errors="aggressive">
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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 <![CDATA[
0bbe34198e24 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
0bbe34198e24 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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5b82f2186244 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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0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 <inputs>
0bbe34198e24 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"/>
0bbe34198e24 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">
0bbe34198e24 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>
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 </param>
0bbe34198e24 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?-->
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 </inputs>
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 <outputs>
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 <data format="tiff" name="output"/>
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 </outputs>
0bbe34198e24 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>
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 <param name="input" value="galaxyIcon_noText.tif"/>
0bbe34198e24 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"/>
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 </test>
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 </tests>
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <help>
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 **What it does**
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31
0bbe34198e24 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.
0bbe34198e24 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/permutate_axis/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 </help>
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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>
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37 </tool>