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annotate detection_viz.xml @ 3:cb2d9de888a1 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
author imgteam
date Wed, 18 Dec 2019 05:02:11 -0500
parents f46f64f9590d
children 99433164b593
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1 <tool id="ip_detection_viz" name="Detection Visualization" version="0.3">
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2 <description>Detection Visualization</description>
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3 <requirements>
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4 <requirement type="package" version="0.14.2">scikit-image</requirement>
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5 <requirement type="package" version="3.0.2">matplotlib</requirement>
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6 <requirement type="package" version="0.15.1">tifffile</requirement>
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7 </requirements>
1
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8 <command detect_errors="aggressive">
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9 <![CDATA[
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10 python '$__tool_directory__/detection_viz.py' '$input' '$output'
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11 --stroke_size $thickness --circle_radius $circle_radius
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12 #if $tp_option['display'] == 'true'
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13 --tp '$tp'
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14 #end if
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15 #if $fn_option['display'] == 'true'
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16 --fn '$fn'
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17 #end if
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18 #if $fp_option['display'] == 'true'
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19 --fp '$fp'
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20 #end if
1
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21 ]]>
0
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22 </command>
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23 <inputs>
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24 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary Image File"/>
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25 <conditional name="tp_option">
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26 <param label="Display true positives" name="display" type="select">
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27 <option selected="True" value="false">No</option>
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28 <option value="true">Yes</option>
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29 </param>
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30 <when value="false"></when>
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31 <when value="true">
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32 <param name="tp" type="data" format="tabular" label="True positives file" />
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33 </when>
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34 </conditional>
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35 <conditional name="fn_option">
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36 <param label="Display false negatives" name="display" type="select">
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37 <option selected="True" value="false">No</option>
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38 <option value="true">Yes</option>
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39 </param>
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40 <when value="false"></when>
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41 <when value="true">
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42 <param name="fn" type="data" format="tabular" label="False negatives file" />
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43 </when>
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44 </conditional>
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45 <conditional name="fp_option">
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46 <param label="Display false positives" name="display" type="select">
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47 <option selected="True" value="false">No</option>
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48 <option value="true">Yes</option>
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49 </param>
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50 <when value="false"></when>
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51 <when value="true">
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52 <param name="fp" type="data" format="tabular" label="False positives file" />
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53 </when>
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54 </conditional>
0
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55 <param name="thickness" type="float" value="3.0" label="Stroke thickness"/>
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56 <param name="circle_radius" type="float" value="50.0" label="Circle radius"/>
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57 </inputs>
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58 <outputs>
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59 <data format="png" name="output"/>
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="input" value="sample.png"/>
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64 <param name="tp_option.display" value="false"/>
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65 <param name="fn_option.display" value="false"/>
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66 <param name="fp_option.display" value="false"/>
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67 <output name="output" value="out.png" ftype="png"/>
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68 </test>
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69 </tests>
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70 <help>
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71 **What it does**
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72
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73 Draws circles of different colors around detected true positives, false negatives and false positives.
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74 </help>
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75 <citations>
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76 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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77 </citations>
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78 </tool>