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annotate gff_feature_colours.xml @ 0:f562c252b285 draft

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planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
author portiahollyoak
date Thu, 26 May 2016 10:48:35 -0400
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children 4f0fb855276c
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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:" />
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6 </stdio>
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7 <command><![CDATA[
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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
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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>
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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>
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29 </param>
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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>
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32 </inputs>
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33 <outputs>
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34 <data format="input" name="output" label="Add feature colours to ${input.element_identifier}" />
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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35 </outputs>
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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36 <help><![CDATA[
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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37 Description
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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38 ------------
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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39
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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40 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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41
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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42 Example
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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43 ----------------
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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44 Input:
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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45
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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46 211000022278978 DHGP Bari1 515 2242 . + . ID=RR41606_transposable_element;
f562c252b285 planemo upload for repository https://github.com/portiahollyoak/Tools commit c31c1a7e9806718e30c9a9036a723e473e09a5eb
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47
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48
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49 Output:
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51 211000022278978 DHGP Bari1 515 2242 . + . ID=RR41606_transposable_element;Colour=#ff00ff;
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52 ]]></help>
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53 </tool>