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annotate projective_transformation.xml @ 5:f5744f0e5a81 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:12:05 +0000
parents 37b079c98c38
children 2f504e075496
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f5744f0e5a81 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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1 <tool id="ip_projective_transformation" name="Performs projective transformation with/without labels" version="0.1.2-2" profile="20.05">
f5744f0e5a81 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ 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>
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5 </edam_operations>
f5744f0e5a81 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ 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>
0
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9 <requirements>
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10 <requirement type="package" version="0.18.1">scikit-image</requirement>
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11 <requirement type="package" version="1.2.4">pandas</requirement>
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12 <requirement type="package" version="1.20.2">numpy</requirement>
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13 <requirement type="package" version="1.6.2">scipy</requirement>
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14 <requirement type="package" version="2020.10.1">tifffile</requirement>
0
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15 </requirements>
1
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16 <command detect_errors="aggressive">
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17 <![CDATA[
3
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18 ln -s '$moving' ./in.${moving.ext} &&
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19 python '$__tool_directory__/projective_transformation.py'
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20 '$fixed'
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21 ./in.${moving.ext}
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22 '$tmat'
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23 ./out.${moving.ext}
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24 && mv ./out.${moving.ext} ./result_image
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param name="moving" type="data" format="tiff,png" label="Moving image (to be transformed)" />
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29 <param name="fixed" type="data" format="tiff,png" label="Fixed image (the reference)" />
be9a815e2240 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit ee372547082b693ef1bbe10b5b7ea8660b9779df"
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30 <param name="tmat" type="data" format="tabular" label="Transformation matrix" />
0
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31 </inputs>
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32 <outputs>
3
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33 <data name="warped" format_source="moving" metadata_source="moving" from_work_dir="result_image" />
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34 </outputs>
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35 <tests>
3
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36 <test>
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37 <param name="fixed" value="fixed.png"/>
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38 <param name="moving" value="moving.png"/>
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39 <param name="tmat" value="tmat.tsv"/>
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40 <output name="warped" value="moving_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" />
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41 </test>
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42 <test>
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43 <param name="fixed" value="fixed_rgb.png"/>
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44 <param name="moving" value="moving_rgb.png"/>
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45 <param name="tmat" value="tmat.tsv"/>
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46 <output name="warped" value="moving_rgb_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" />
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47 </test>
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48 <test>
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49 <param name="fixed" value="multi_f.tif"/>
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50 <param name="moving" value="multi_m.tif"/>
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51 <param name="tmat" value="tmat.tsv"/>
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52 <output name="warped" value="multi_m_warped.tif" ftype="tiff" compare="sim_size" delta_frac="0.1" />
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53 </test>
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54 </tests>
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55 <help>
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56
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57 **What it does**
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58
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f5744f0e5a81 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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59 This tool performs a projective transformation of the moving 2D image so that it fits the fixed 2D image.
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60 Multi-channel and RGB images are supported.
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61 </help>
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62 <citations>
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63 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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64 </citations>
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65 </tool>