Mercurial > repos > galaxyp > gffcompare_to_bed
comparison gffcompare_to_bed.xml @ 0:7e572e148175 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
author | galaxyp |
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date | Thu, 11 Jan 2018 11:16:51 -0500 |
parents | |
children | 0f62097d7c1a |
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1 <tool id="gffcompare_to_bed" name="Convert gffCompare annotated GTF to BED" version="0.1.0"> | |
2 <description>for StringTie results</description> | |
3 <command detect_errors="exit_code"><![CDATA[ | |
4 python '$__tool_directory__/gffcompare_to_bed.py' | |
5 #if $class_codes: | |
6 --class_code='$class_codes' | |
7 #end if | |
8 $input $output | |
9 ]]></command> | |
10 <inputs> | |
11 <param name="input" type="data" format="gtf" label="GTF annotated by gffCompare"/> | |
12 <param name="class_codes" type="select" display="checkboxes" multiple="true" optional="true" | |
13 label="filter gffCompare class_codes to convert" help="No selection implies no filtering"> | |
14 <option value="=">= : Complete match of intron chain</option> | |
15 <option value="c">c : Contained</option> | |
16 <option value="j">j : Potentially novel isoform (fragment): at least one splice junction is shared with a reference transcript</option> | |
17 <option value="e">e : Single exon transfrag overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.</option> | |
18 <option value="i">i : A transfrag falling entirely within a reference intron</option> | |
19 <option value="o">o : Generic exonic overlap with a reference transcript</option> | |
20 <option value="p">p : Possible polymerase run-on fragment (within 2Kbases of a reference transcript)</option> | |
21 <option value="r">r : Repeat. Currently determined by looking at the soft-masked reference sequence and applied to transcripts where at least 50% of the bases are lower case</option> | |
22 <option value="u">u : Unknown, intergenic transcript</option> | |
23 <option value="x">x : Exonic overlap with reference on the opposite strand</option> | |
24 <option value="s">s : An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors)</option> | |
25 </param> | |
26 </inputs> | |
27 <outputs> | |
28 <data name="output" format="bed" /> | |
29 </outputs> | |
30 <tests> | |
31 <test> | |
32 <param name="input" value="gffcompare_annotated.gtf" ftype="gtf"/> | |
33 <output name="output" file="gffcompare_output.bed"/> | |
34 </test> | |
35 <test> | |
36 <param name="input" value="gffcompare_annotated.gtf" ftype="gtf"/> | |
37 <param name="class_codes" value="j"/> | |
38 <output name="output" file="gffcompare_output_j.bed"/> | |
39 </test> | |
40 <test> | |
41 <param name="input" value="gffcompare_annotated.gtf" ftype="gtf"/> | |
42 <param name="class_codes" value="j,e,i,p,u,x"/> | |
43 <output name="output" file="gffcompare_output_jeipux.bed"/> | |
44 </test> | |
45 | |
46 </tests> | |
47 <help><![CDATA[ | |
48 Convert a GFFCompare annotated GTF file to BED format. | |
49 | |
50 usage: gffcompare_to_bed.py [-h] [-C CLASS_CODE] [-v] [-d] input output | |
51 | |
52 positional arguments: | |
53 input GFFCompare annotated GTF file, (-) for stdin | |
54 output BED file, (-) for stdout | |
55 | |
56 optional arguments: | |
57 -h, --help show this help message and exit | |
58 -C CLASS_CODE, --class_code CLASS_CODE | |
59 Restrict output to gffcompare class codes | |
60 -d, --debug Debug | |
61 | |
62 ]]></help> | |
63 <citations> | |
64 <citation type="doi">10.1038/nbt.1621</citation> | |
65 </citations> | |
66 </tool> |