Mercurial > repos > galaxyp > gffcompare_to_bed
comparison gffcompare_to_bed.xml @ 1:0f62097d7c1a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit e5ab6444aa2f104eedfa366bee05f65edef02d82
author | galaxyp |
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date | Fri, 26 Apr 2019 14:42:31 -0400 |
parents | 7e572e148175 |
children | 9a4cfc910674 |
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0:7e572e148175 | 1:0f62097d7c1a |
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1 <tool id="gffcompare_to_bed" name="Convert gffCompare annotated GTF to BED" version="0.1.0"> | 1 <tool id="gffcompare_to_bed" name="Convert gffCompare annotated GTF to BED" version="0.2.0"> |
2 <description>for StringTie results</description> | 2 <description>for StringTie results</description> |
3 <command detect_errors="exit_code"><![CDATA[ | 3 <command detect_errors="exit_code"><![CDATA[ |
4 python '$__tool_directory__/gffcompare_to_bed.py' | 4 python '$__tool_directory__/gffcompare_to_bed.py' |
5 #if $class_codes: | 5 #if $class_codes: |
6 --class_code='$class_codes' | 6 --class_code='$class_codes' |
10 <inputs> | 10 <inputs> |
11 <param name="input" type="data" format="gtf" label="GTF annotated by gffCompare"/> | 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" | 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"> | 13 label="filter gffCompare class_codes to convert" help="No selection implies no filtering"> |
14 <option value="=">= : Complete match of intron chain</option> | 14 <option value="=">= : Complete match of intron chain</option> |
15 <option value="~">~ : Intron chain match or single-exon (gffcompare strict-match)</option> | |
15 <option value="c">c : Contained</option> | 16 <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="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="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="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="o">o : Generic exonic overlap with a reference transcript</option> |
45 | 46 |
46 </tests> | 47 </tests> |
47 <help><![CDATA[ | 48 <help><![CDATA[ |
48 Convert a GFFCompare annotated GTF file to BED format. | 49 Convert a GFFCompare annotated GTF file to BED format. |
49 | 50 |
51 A typical workflow: | |
52 | |
53 .. image:: GTF2Bed_workflow.png | |
54 :height: 308 | |
55 :width: 750 | |
56 | |
50 usage: gffcompare_to_bed.py [-h] [-C CLASS_CODE] [-v] [-d] input output | 57 usage: gffcompare_to_bed.py [-h] [-C CLASS_CODE] [-v] [-d] input output |
51 | 58 |
52 positional arguments: | 59 positional arguments: |
53 input GFFCompare annotated GTF file, (-) for stdin | 60 input GFFCompare annotated GTF file, (-) for stdin |
54 output BED file, (-) for stdout | 61 output BED file, (-) for stdout |
57 -h, --help show this help message and exit | 64 -h, --help show this help message and exit |
58 -C CLASS_CODE, --class_code CLASS_CODE | 65 -C CLASS_CODE, --class_code CLASS_CODE |
59 Restrict output to gffcompare class codes | 66 Restrict output to gffcompare class codes |
60 -d, --debug Debug | 67 -d, --debug Debug |
61 | 68 |
69 For class_code definitions see gffcompare documentation: | |
70 http://ccb.jhu.edu/software/stringtie/gffcompare.shtml#transfrag-class-codes | |
71 | |
62 ]]></help> | 72 ]]></help> |
63 <citations> | 73 <citations> |
64 <citation type="doi">10.1038/nbt.1621</citation> | 74 <citation type="doi">10.1038/nbt.1621</citation> |
65 </citations> | 75 </citations> |
66 </tool> | 76 </tool> |