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planemo upload for repository https://github.com/portiahollyoak/Tools commit 5f5802314b55f52ea4b3f9f515ec46a5a770696d-dirty
author portiahollyoak
date Thu, 26 May 2016 11:07:21 -0400
parents f562c252b285
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f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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1 <tool id="gff_feature_colours" name="Add Feature Colours to GFF" version="0.1.0">
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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2 <requirements>
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3 </requirements>
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4 <stdio>
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5 <exit_code range="1:" />
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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6 </stdio>
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7 <command><![CDATA[
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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8 python "$__tool_directory__"/add_colour.py
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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9 --input $input
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10 --features
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11 #for feature in $feat
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12 "${feature.feature}"
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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13 #end for
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14 --colours
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15 #for feature in $feat
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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16 "${feature.feature_colour.value}"
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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17 #end for
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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18 --output $output
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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19 ]]></command>
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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20 <inputs>
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21 <param name="input" type="data" format="gff,gtf" label="Dataset"/>
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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22 <repeat name="feat" title="Feature to assign a colour">
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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23 <param name="feature" type="select">
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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24 <options from_dataset="input">
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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25 <column name="name" index="2"/>
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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26 <column name="value" index="2"/>
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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27 <filter type="unique_value" ref="input" column="2" />
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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28 </options>
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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29 </param>
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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30 <param name="feature_colour" type="color" label="Feature Colour" value="#ff00ff"/>
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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31 </repeat>
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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32 </inputs>
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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33 <outputs>
1
4f0fb855276c planemo upload for repository https://github.com/portiahollyoak/Tools commit 5f5802314b55f52ea4b3f9f515ec46a5a770696d-dirty
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34 <data format_source="input" name="output" label="Add feature colours to ${input.element_identifier}" />
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f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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35 </outputs>
1
4f0fb855276c planemo upload for repository https://github.com/portiahollyoak/Tools commit 5f5802314b55f52ea4b3f9f515ec46a5a770696d-dirty
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36 <tests>
4f0fb855276c planemo upload for repository https://github.com/portiahollyoak/Tools commit 5f5802314b55f52ea4b3f9f515ec46a5a770696d-dirty
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37 <test>
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38 <param name="input" value="test-gff.gff" ftype="gff"/>
4f0fb855276c planemo upload for repository https://github.com/portiahollyoak/Tools commit 5f5802314b55f52ea4b3f9f515ec46a5a770696d-dirty
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39 <param name="feat_0|feature" value="Idefix" />
4f0fb855276c planemo upload for repository https://github.com/portiahollyoak/Tools commit 5f5802314b55f52ea4b3f9f515ec46a5a770696d-dirty
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40 <param name="feat_0|feature_colour" value="#ff0000"/>
4f0fb855276c planemo upload for repository https://github.com/portiahollyoak/Tools commit 5f5802314b55f52ea4b3f9f515ec46a5a770696d-dirty
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41 <param name="feat_1|feature" value="INE-1" />
4f0fb855276c planemo upload for repository https://github.com/portiahollyoak/Tools commit 5f5802314b55f52ea4b3f9f515ec46a5a770696d-dirty
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42 <param name="feat_1|feature_colour" value="#00ff00"/>
4f0fb855276c planemo upload for repository https://github.com/portiahollyoak/Tools commit 5f5802314b55f52ea4b3f9f515ec46a5a770696d-dirty
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43 <output name="output" file="test-gff-colours.gff" ftype="gff"/>
4f0fb855276c planemo upload for repository https://github.com/portiahollyoak/Tools commit 5f5802314b55f52ea4b3f9f515ec46a5a770696d-dirty
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44 </test>
4f0fb855276c planemo upload for repository https://github.com/portiahollyoak/Tools commit 5f5802314b55f52ea4b3f9f515ec46a5a770696d-dirty
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45 </tests>>
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f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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46 <help><![CDATA[
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47 Description
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48 ------------
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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49
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50 The Add Feature Colours tool allows the user to assign a colour to unique features found in the 3rd column of a GFF file for visualisation in a genome browser. It works by allowing the user to match unique features to a colour and then it will add the assigned colour of that feature to the 9th column of the feature line. This will then be interpreted by the genome browser, and the feature will appear in its assigned colour.
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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51
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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52 Example
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53 ----------------
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54 Input:
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55
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56 211000022278978 DHGP Bari1 515 2242 . + . ID=RR41606_transposable_element;
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57
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58
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59 Output:
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60
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61 211000022278978 DHGP Bari1 515 2242 . + . ID=RR41606_transposable_element;Colour=#ff00ff;
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62 ]]></help>
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63 </tool>