Mercurial > repos > goeckslab > backsub
annotate backsub.xml @ 0:bf9f98a7f936 draft default tip
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
author | goeckslab |
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date | Wed, 05 Jun 2024 18:01:54 +0000 |
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bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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1 <tool id="backsub" name="Background subtraction" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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2 |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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3 <description>for sequential immunofluorescence images</description> |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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4 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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5 <macros> |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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6 <import>macros.xml</import> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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7 </macros> |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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8 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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9 <expand macro="requirements"/> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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10 <expand macro="version_cmd"/> |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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11 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
goeckslab
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12 <command detect_errors="aggressive"><![CDATA[ |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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13 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
goeckslab
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14 python /background_subtraction/background_sub.py |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
goeckslab
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15 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
goeckslab
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16 ##Supply image |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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17 --root '$root' |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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18 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
goeckslab
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19 ##Supply markers |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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20 --markers '$markers' |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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21 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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22 ##Name output image file |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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23 --output out.ome.tiff |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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24 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
goeckslab
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25 ##Name output markers file |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
goeckslab
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26 --marker-output out.csv |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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27 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
goeckslab
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28 ##Additional arguments |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
goeckslab
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29 #if $adv.pixel_size |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
goeckslab
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30 --pixel-size $adv.pixel_size |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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31 #end if |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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32 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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33 #if $adv.tile_size |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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34 --tile-size $adv.tile_size |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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35 #end if |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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36 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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37 ]]></command> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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38 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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39 <inputs> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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40 <param name="root" type="data" format="ome.tiff" optional="false" label="Image to process"/> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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41 <param name="markers" type="data" format="csv" optional="false" label="Markers file mapping channels to subtract" help="Expected columns: marker_name, background, exposure, remove"/> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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42 <section name="adv" title="Advanced Options" expanded="false"> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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43 <param name="pixel_size" type="float" optional="true" min=".01" max="1.0" label="Pixel size in microns" help="If not supplied, finds resolution in XML metadata, otherwise defaults to 1"/> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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44 <param name="tile_size" type="integer" optional="true" min="256" max="2048" label="Tile size for pyramid generation (default 1024)"/> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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45 </section> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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46 </inputs> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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47 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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48 <outputs> |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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49 <data format="ome.tiff" name="image_output" from_work_dir="out.ome.tiff" label="${tool.name} on ${on_string}: Subtracted Image"/> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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50 <data format="csv" name="marker_output" from_work_dir="out.csv" label="${tool.name} on ${on_string}: Markers"/> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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51 </outputs> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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52 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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53 <tests> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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54 <test expect_num_outputs="2"> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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55 <param name="root" value="test.ome.tiff" /> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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56 <param name="markers" value="test_markers.csv" /> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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57 <param name="tile_size" value="256" /> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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58 <output name="image_output" ftype="ome.tiff"> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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59 <assert_contents> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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60 <has_size value="520000" delta="10000" /> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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61 </assert_contents> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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62 </output> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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63 <output name="marker_output" ftype="csv"> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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64 <assert_contents> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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65 <has_n_columns n="3" sep="," /> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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66 <has_n_lines n="3" /> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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67 </assert_contents> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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68 </output> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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69 </test> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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70 </tests> |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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71 <help><![CDATA[ |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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72 **Background autofluorescence subtraction for cyclic imaging data** |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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73 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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74 Performs Pixel-by-pixel channel subtraction scaled by exposure times |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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75 primarily developed for images produced by the COMET platform and to work within |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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76 the MCMICRO pipeline. Main usecase is autuofluorescence subtraction for |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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77 multichannel and multicycle images for visualization of images from tissues with |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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78 high autofluroescence (FFPE), improved segmentation, and quantification (if the |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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79 previous two usecases aren't necessary, downstream subtraction of |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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80 autofluorescent signal is encouraged as the script is memory inefficent). |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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81 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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82 The markers file (CSV) gives details about the channels and needs to contain |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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83 the following columns: "marker_name", "background", "exposure", "remove" |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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84 |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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85 The "marker_name" column should indicate the marker for the acquired channel and all values should be unique. |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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86 The "background" column should indicate the marker name of the channel which needs to be subtracted. |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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87 This value must match the "marker_name" value of the background channel. |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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88 The "exposure" column should contain the exposure time used for channel acquisition, |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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89 and the measure unit should be consistent across the column. Exposure time is used for scaling the |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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90 value of the background to be comparable to the processed channel. The "remove" column should contain |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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91 logical `TRUE` values for channels which should be exluded in the output image. |
bf9f98a7f936
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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92 |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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93 *Visit https://github.com/SchapiroLabor/Background_subtraction/ for the most up-to-date information* |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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94 ]]></help> |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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95 <expand macro="citations" /> |
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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/background-subtraction commit 7030070398b2b137b40f7893a82bd9889ae9df6f
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96 </tool> |