Mercurial > repos > petr-novak > repeat_annotation_pipeline3

annotate compare_gff.xml @ 8:2557cad81607 draft

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author petr-novak
date Wed, 03 May 2023 11:12:41 +0000
parents b53f5a456d01
children 5366d5ea04bc
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1 <tool id="compare_gff" name="Compare overlap of two GFF3" version="0.1.0" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package">bioconductor-rtracklayer</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 $__tool_directory__/compare_gff.R '$input1_gff' '$input2_gff' '$attribute_name'
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7 &&
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8 cp annotation_overlap_long.csv '$out_long'
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9 &&
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10 cp annotation_overlap.csv '$out_wide'
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11
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12 ]]></command>
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13 <inputs>
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14 <param type="data" name="input1_gff" format="gff" label="First GFF">
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15 <sanitizer invalid_char="">
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16 <valid initial="string.ascii_letters,string.digits">
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17 <add value="_" />
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18 </valid>
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19 </sanitizer>
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20 </param>
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21 <param type="data" name="input2_gff" format="gff" label="Second GFF">
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22 <sanitizer invalid_char="">
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23 <valid initial="string.ascii_letters,string.digits">
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24 <add value="_" />
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25 </valid>
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26 </sanitizer>
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27 </param>
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28 <param type="text" name="attribute_name" label="Name of attribute to summarize"/>
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29 </inputs>
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30 <outputs>
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31 <data name="out_long" format="tabular" label="Overlap of annotations
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32 ${input1_gff.hid} and ${input1_gff.hid} (as matrix)" />
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33 <data name="out_wide" format="tabular" label="Overlap of annotations
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34 ${input1_gff.hid} and ${input1_gff.hid} (as table)"/>
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35 </outputs>
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36 <help><![CDATA[
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37 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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38 ]]></help>
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39 </tool>