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annotate projective_transformation.xml @ 4:37b079c98c38 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit ded1703bcd6e295b26201505edb58381991b265e"
author imgteam
date Mon, 28 Feb 2022 17:36:23 +0000
parents be9a815e2240
children f5744f0e5a81
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37b079c98c38 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit ded1703bcd6e295b26201505edb58381991b265e"
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1 <tool id="ip_projective_transformation" name="Projective Transformation" version="0.1.2" profile="20.05">
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2 <description>of 2D images</description>
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3 <requirements>
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4 <requirement type="package" version="0.18.1">scikit-image</requirement>
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5 <requirement type="package" version="1.2.4">pandas</requirement>
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6 <requirement type="package" version="1.20.2">numpy</requirement>
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7 <requirement type="package" version="1.6.2">scipy</requirement>
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8 <requirement type="package" version="2020.10.1">tifffile</requirement>
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9 </requirements>
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10 <command detect_errors="aggressive">
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11 <![CDATA[
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12 ln -s '$moving' ./in.${moving.ext} &&
be9a815e2240 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit ee372547082b693ef1bbe10b5b7ea8660b9779df"
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13 python '$__tool_directory__/projective_transformation.py'
be9a815e2240 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit ee372547082b693ef1bbe10b5b7ea8660b9779df"
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14 '$fixed'
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15 ./in.${moving.ext}
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16 '$tmat'
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17 ./out.${moving.ext}
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18 && mv ./out.${moving.ext} ./result_image
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param name="moving" type="data" format="tiff,png" label="Moving image (to be transformed)" />
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23 <param name="fixed" type="data" format="tiff,png" label="Fixed image (the reference)" />
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24 <param name="tmat" type="data" format="tabular" label="Transformation matrix" />
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25 </inputs>
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26 <outputs>
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27 <data name="warped" format_source="moving" metadata_source="moving" from_work_dir="result_image" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="fixed" value="fixed.png"/>
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32 <param name="moving" value="moving.png"/>
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33 <param name="tmat" value="tmat.tsv"/>
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34 <output name="warped" value="moving_warped.png" ftype="png" compare="sim_size" delta_frac="0.1" />
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35 </test>
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36 <test>
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37 <param name="fixed" value="fixed_rgb.png"/>
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38 <param name="moving" value="moving_rgb.png"/>
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39 <param name="tmat" value="tmat.tsv"/>
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40 <output name="warped" value="moving_rgb_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="multi_f.tif"/>
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44 <param name="moving" value="multi_m.tif"/>
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45 <param name="tmat" value="tmat.tsv"/>
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46 <output name="warped" value="multi_m_warped.tif" ftype="tiff" compare="sim_size" delta_frac="0.1" />
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47 </test>
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48 </tests>
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49 <help>
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50
be9a815e2240 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/projective_transformation/ commit ee372547082b693ef1bbe10b5b7ea8660b9779df"
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51 **What it does**
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52
2
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53 This tool performs a projective transformation of the moving image so that it fits the fixed image.
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54 Multi-channel and RGB images are supported.
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55 </help>
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56 <citations>
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57 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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58 </citations>
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59 </tool>