Mercurial > repos > petr-novak > repeat_annotation_pipeline3

annotate compare_gff.xml @ 12:755a4d643184 draft default tip

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planemo upload commit a61591d548f42ff417781e7fe7418dc2901ccc23
author petr-novak
date Tue, 26 Sep 2023 07:28:04 +0000
parents 5366d5ea04bc
children
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1 <tool id="compare_gff" name="Compare overlap of two GFF3" version="0.1.0"
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2 python_template_version="3.5">
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3 <requirements>
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4 <requirement type="package">bioconductor-rtracklayer</requirement>
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5 </requirements>
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6 <required_files>
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7 <include type="literal" path="compare_gff.R"/>
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8 </required_files>
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9 <command detect_errors="exit_code"><![CDATA[
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10 Rscript '$__tool_directory__'/compare_gff.R '$input1_gff' '$input2_gff' '$attribute_name'
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11 &&
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12 cp annotation_overlap_long.csv '$out_long'
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13 &&
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14 cp annotation_overlap.csv '$out_wide'
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16 ]]></command>
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17 <inputs>
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18 <param type="data" name="input1_gff" format="gff" label="First GFF">
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19 <sanitizer invalid_char="">
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20 <valid initial="string.ascii_letters,string.digits">
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21 <add value="_"/>
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22 </valid>
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23 </sanitizer>
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24 </param>
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25 <param type="data" name="input2_gff" format="gff" label="Second GFF">
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26 <sanitizer invalid_char="">
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27 <valid initial="string.ascii_letters,string.digits">
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28 <add value="_"/>
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29 </valid>
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30 </sanitizer>
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31 </param>
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32 <param type="text" name="attribute_name" label="Name of attribute to summarize"
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33 optional="false" default="Name"/>
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34 </inputs>
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35 <outputs>
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36 <data name="out_long" format="tabular" label="Overlap of annotations
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37 ${input1_gff.hid} and ${input1_gff.hid} (as matrix)"/>
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38 <data name="out_wide" format="tabular" label="Overlap of annotations
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39 ${input1_gff.hid} and ${input1_gff.hid} (as table)"/>
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40 </outputs>
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41 <help><![CDATA[
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42 Compare overlaps in two GFF3 by selected attribute. Overlap is reported a number of bases. It expects not overlap within individuals GFF3.
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43 ]]></help>
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44 </tool>