Mercurial > repos > thomaswollmann > points2binaryimage

annotate points2binaryimage.xml @ 0:74b946cdba21 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
author thomaswollmann
date Wed, 12 Dec 2018 04:51:33 -0500
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74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
thomaswollmann
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1 <tool id="points2binaryimage" name="Points to Binary Image" version="0.1">
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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2 <description>Converts points to a binary image</description>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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3 <requirements>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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4 <requirement type="package" version="0.14.1" >scikit-image</requirement>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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5 <requirement type="package" version="1.15.4">numpy</requirement>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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6 <requirement type="package" version="0.23.4">pandas</requirement>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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7 <requirement type="package" version="2018.7">pytz</requirement><!--pandas seems to have additional requirements that are not automatically installed-->
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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8 <requirement type="package" version="2.4.1">dateutil</requirement>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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9 </requirements>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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10 <command>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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11 <![CDATA[
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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12 python '$__tool_directory__/points2binaryimage.py' '$input' '$output' $shapex $shapey $has_header $invert_xy
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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13 ]]>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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14 </command>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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15 <inputs>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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16 <param name="input" type="data" format="csv" label="CSV point file"/>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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17 <param name="shapex" type="integer" value="500" optional="true" min="1" max="2000" label="Width of output image" />
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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18 <param name="shapey" type="integer" value="500" optional="true" min="1" max="2000" label="Height of output image" />
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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19 <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" />
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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20 <param name="invert_xy" type="boolean" checked="false" falsevalue="" truevalue="--invert_xy True" optional="true" label="Inverts x and y in CSV point file" />
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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21 </inputs>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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22 <outputs>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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23 <data name="output" format="tiff" />
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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24 </outputs>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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25 <tests>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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26 <test>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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27 <param name="input" value="points.csv" />
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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28 <param name="shapex" value="20" />
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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29 <param name="shapey" value="30" />
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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30 <param name="has_header" value="false" />
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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31 <param name="invert_xy" value="true" />
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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32 <output name="output" ftype="tiff" file="out.tiff" compare="sim_size"/>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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33 </test>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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34 </tests>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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35 <help>Converts CSV point file to binary image.</help>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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36 <citations>
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37 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
74b946cdba21 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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38 </citations>
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39 </tool>