Mercurial > repos > cpt > cpt_remove_annotations
comparison cpt_rem_annotes/remove_annotations.xml @ 0:03d27abd1dfd draft
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author | cpt |
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date | Fri, 13 May 2022 05:26:10 +0000 |
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-1:000000000000 | 0:03d27abd1dfd |
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1 <?xml version="1.0"?> | |
2 <tool id="edu.tamu.cpt.gff3.remove_annots" name="Remove Annotation Feature" version="19.1.0.1" profile="16.04"> | |
3 <description>that's unused in our GFF tools</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 <import>cpt-macros.xml</import> | |
7 </macros> | |
8 <expand macro="requirements"/> | |
9 <command detect_errors="aggressive"><![CDATA[ | |
10 python $__tool_directory__/remove_annotations.py | |
11 $gff3_data | |
12 $remark | |
13 $region | |
14 > $default]]></command> | |
15 <inputs> | |
16 <expand macro="gff3_input" /> | |
17 <param checked="true" label="Remove 'remark' features" name="remark" type="boolean" truevalue="--remark" falsevalue="" /> | |
18 <param checked="true" label="Remove 'region' features" name="region" type="boolean" truevalue="--region" falsevalue="" /> | |
19 </inputs> | |
20 <outputs> | |
21 <data format="gff3" name="default"/> | |
22 </outputs> | |
23 <tests> | |
24 <test> | |
25 <param name="gff3_data" value="RemoveAnnote_In.gff3" /> | |
26 <param name="remark" value="--remark" /> | |
27 <param name="region" value= "--region" /> | |
28 <output name="default" file="RemoveAnnote_Out.gff3" /> | |
29 </test> | |
30 </tests> | |
31 <help><![CDATA[ | |
32 **What it does** | |
33 | |
34 For an input GFF3, this tool specifically removes the feature entry with remark and/or region type (column 3) as needed for compatibility | |
35 with certain tools. These feature typically encompasses the entire length of the sequence upon which the GFF3 is based. | |
36 | |
37 Example input: | |
38 Miro annotation remark 1 167935 . . . gff-version=3;sequence-region=%28%27Miro%27%2C 0%2C 172788%29 | |
39 | |
40 Miro cpt gene 1231 5436 . . . ID=CDS1; | |
41 | |
42 Example output: | |
43 Miro cpt gene 1231 5436 . . . ID=CDS1; | |
44 | |
45 | |
46 ]]></help> | |
47 <expand macro="citations" /> | |
48 </tool> |