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annotate points2label.xml @ 2:30ca5d5d03ec draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:11:46 +0000
parents 9bd039f46843
children de611b3b5ae8
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30ca5d5d03ec planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
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1 <tool id="ip_points_to_label" name="Convert point coordinates to label map" version="0.3-2">
30ca5d5d03ec planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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2 <description></description>
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3 <edam_operations>
30ca5d5d03ec planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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4 <edam_operation>operation_3443</edam_operation>
30ca5d5d03ec planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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5 </edam_operations>
30ca5d5d03ec planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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6 <xrefs>
30ca5d5d03ec planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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7 <xref type="bio.tools">galaxy_image_analysis</xref>
30ca5d5d03ec planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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8 </xrefs>
0
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 <requirements>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10 <requirement type="package" version="1.15.4">numpy</requirement>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 <requirement type="package" version="0.14.2">scikit-image</requirement>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 <requirement type="package" version="0.23.4">pandas</requirement>
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9bd039f46843 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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13 <requirement type="package" version="0.15.1">tifffile</requirement>
9bd039f46843 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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14 </requirements>
9bd039f46843 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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15 <command detect_errors="aggressive">
0
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 <![CDATA[
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 python '$__tool_directory__/points2label.py' '$input' '$output' '$org_file' $has_header
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 ]]>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 </command>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 <inputs>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 <param name="input" type="data" format="tabular" label="Point CSV file"/>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 <param name="org_file" type="data" format="tiff" label="Original label image file"/>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" />
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 </inputs>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 <outputs>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <data name="output" format="tiff"/>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 </outputs>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 <tests>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <test>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 <param name="input" value="points.tsv"/>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 <param name="org_file" value="galaxyIcon_noText.tif"/>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 <output name="output" file="out.tif" ftype="tiff" compare="sim_size"/>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 </test>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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34 </tests>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 <help>
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36 **What it does**
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 This tool converts points to a label image.
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 </help>
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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40 <citations>
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41 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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42 </citations>
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43 </tool>