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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:12:09 +0000
parents 3a686b6aa7fc
children 499ad4d9aa13
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65e95d0b8838 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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1 <tool id="ip_projective_transformation_points" name="Performs projective transformation" license="MIT" version="0.1.1-2" profile="20.05">
65e95d0b8838 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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2 <description></description>
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3 <edam_operations>
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4 <edam_operation>operation_3443</edam_operation>
65e95d0b8838 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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5 </edam_operations>
65e95d0b8838 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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6 <xrefs>
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7 <xref type="bio.tools">galaxy_image_analysis</xref>
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8 </xrefs>
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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9 <requirements>
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10 <requirement type="package" version="0.14.2">scikit-image</requirement>
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0d2707c82d29 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit f1298dca5a7f5be3acbb5e3d80c98b1cd6d2795b"
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11 <requirement type="package" version="1.2.1">scipy</requirement>
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 <requirement type="package" version="0.23.4">pandas</requirement>
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aaac58d83043 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit 7391bb4256f49ec30cf38d9438f97e11ec25a115"
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13 <requirement type="package" version="1.15.2">numpy</requirement>
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0d2707c82d29 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit f1298dca5a7f5be3acbb5e3d80c98b1cd6d2795b"
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14 <requirement type="package" version="0.15.1">tifffile</requirement>
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 </requirements>
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16 <command detect_errors="aggressive">
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17 <![CDATA[
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 python '$__tool_directory__/projective_transformation_points.py'
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19 '$input'
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20 '$tmat'
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21 '$output'
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22 ]]>
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 </command>
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 <inputs>
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25 <param name="input" type="data" format="tabular" label="ROIs (pixel coordinates) to be transformed (TSV file)" />
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26 <param name="tmat" type= "data" format="tabular" label="Transformation matrix (TSV file)" />
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 </inputs>
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 <outputs>
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29 <data format="tabular" name="output" />
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30 </outputs>
0
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31 <tests>
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32 <test>
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33 <param name="input" value="in.tabular" />
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34 <param name="tmat" value="tmat.tabular" />
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35 <output name="output" value="out.tabular" ftype="tabular" compare="diff" />
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ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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36 </test>
ed8a71e13f7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation_points/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 </tests>
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38 <help>
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39 **What it does**
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40
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41 This tool performs a projective transformation of regions of interest (ROIs) defined by pixel (point) coordinates with/without labels.
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42
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43 About the format of point coordinates (and labels) in the input TSV table:
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44 1st column: x-coordinate;
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45 2nd column: y-coordinate;
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46 (optional) more column(s): point label(s) (numerical or categorical).
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47 The top row of the table will be regarded as column headers.
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48
0
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49 </help>
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50 <citations>
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51 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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52 </citations>
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53 </tool>