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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 356f2556bd629e5473d6711ec71372ea17d3e28f
author thomaswollmann
date Wed, 12 Dec 2018 05:11:33 -0500
parents fae4e354c2da
children
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eab836c5078c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 356f2556bd629e5473d6711ec71372ea17d3e28f
thomaswollmann
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1 <tool id="points2labelimage" name="Points 2 Label" version="0.2">
0
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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2 <description>Points to Label Image</description>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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3 <requirements>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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4 <requirement type="package" version="1.15.4">numpy</requirement>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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5 <requirement type="package" version="0.14.0">scikit-image</requirement>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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6 <requirement type="package" version="0.23.4">pandas</requirement>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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7 </requirements>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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8 <command>
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9 <![CDATA[
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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10 python '$__tool_directory__/points2label.py' '$input' '$output' '$org_file' $has_header $is_tsv
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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11 ]]>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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12 </command>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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13 <inputs>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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14 <param name="input" type="data" format="csv" label="Point CSV file"/>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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15 <param name="org_file" type="data" format="tiff" label="Original label image file"/>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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16 <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" />
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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17 <param name="is_tsv" optional="true" type="boolean" checked="false" truevalue="--is_tsv True" falsevalue="" help="tab separated input file"/>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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18 </inputs>
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19 <outputs>
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20 <data name="output" format="tiff"/>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input" value="points.csv"/>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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25 <param name="org_file" value="galaxyIcon_noText.tif"/>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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26 <output name="output" file="out.tif" ftype="tiff" compare="sim_size"/><!--to allow a change in e.g. date-->
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27 </test>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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28 </tests>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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29 <help> This tool converts points to a label image. </help>
fae4e354c2da planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0
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30 <citations>
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31 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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32 </citations>
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33 </tool>