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annotate points2binaryimage.xml @ 1:90385ec28b34 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:11:42 +0000
parents dd513c9f5230
children 2ad6350df85b
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90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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1 <tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="0.2-1">
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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2 <description></description>
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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3 <edam_operations>
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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4 <edam_operation>operation_3443</edam_operation>
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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5 </edam_operations>
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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6 <xrefs>
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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7 <xref type="bio.tools">galaxy_image_analysis</xref>
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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8 </xrefs>
0
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 <requirements>
1
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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10 <requirement type="package" version="0.14.2">scikit-image</requirement>
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dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 <requirement type="package" version="1.15.4">numpy</requirement>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 <requirement type="package" version="0.23.4">pandas</requirement>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 <requirement type="package" version="2018.7">pytz</requirement><!--pandas seems to have additional requirements that are not automatically installed-->
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 <requirement type="package" version="2.4.1">dateutil</requirement>
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90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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15 <requirement type="package" version="0.15.1">tifffile</requirement>
0
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 </requirements>
1
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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17 <command detect_errors="aggressive">
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dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 <![CDATA[
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 python '$__tool_directory__/points2binaryimage.py' '$input' '$output' $shapex $shapey $has_header $invert_xy
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 ]]>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 </command>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 <inputs>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <param name="input" type="data" format="tabular" label="CSV point file"/>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 <param name="shapex" type="integer" value="500" optional="true" min="1" max="2000" label="Width of output image" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 <param name="shapey" type="integer" value="500" optional="true" min="1" max="2000" label="Height of output image" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 <param name="invert_xy" type="boolean" checked="false" falsevalue="" truevalue="--invert_xy True" optional="true" label="Inverts x and y in CSV point file" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 </inputs>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <outputs>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 <data name="output" format="tiff" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 </outputs>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 <tests>
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33 <test>
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34 <param name="input" value="points.tsv" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 <param name="shapex" value="20" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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36 <param name="shapey" value="30" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 <param name="has_header" value="false" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 <param name="invert_xy" value="true" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 <output name="output" ftype="tiff" file="out.tiff" compare="sim_size"/>
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40 </test>
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41 </tests>
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42 <help>
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43 **What it does**
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44
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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45 Converts CSV point file to binary image.
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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46 </help>
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47 <citations>
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48 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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49 </citations>
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50 </tool>