Mercurial > repos > nilesh > rseqc
annotate junction_annotation.xml @ 51:09846d5169fa draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author | iuc |
---|---|
date | Tue, 14 Mar 2017 10:23:21 -0400 |
parents | 6b33e31bda10 |
children | 34e4c586e3c0 |
rev | line source |
---|---|
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
1 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="@WRAPPER_VERSION@"> |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
2 <description>compares detected splice junctions to reference gene model</description> |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
3 |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
4 <macros> |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
5 <import>rseqc_macros.xml</import> |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
6 </macros> |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
7 |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
8 <expand macro="requirements" /> |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
9 |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
10 <expand macro="stdio" /> |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
11 |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
12 <version_command><![CDATA[junction_annotation.py --version]]></version_command> |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
13 |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
14 <command><![CDATA[ |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
15 junction_annotation.py |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
16 --input-file '${input}' |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
17 --refgene '${refgene}' |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
18 --out-prefix output |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
19 --min-intron ${min_intron} |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
20 --mapq ${mapq} |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
21 ]]> |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
22 </command> |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
23 |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
24 <inputs> |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
25 <expand macro="bam_sam_param" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
26 <expand macro="refgene_param" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
27 <expand macro="min_intron_param" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
28 <expand macro="mapq_param" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
29 <expand macro="rscript_output_param" /> |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
30 </inputs> |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
31 |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
32 <outputs> |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
33 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events pdf)"/> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
34 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction pdf)" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
35 <expand macro="xls_output_data" filename="output.junction.xls" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
36 <expand macro="rscript_output_data" filename="output.junction_plot.r" /> |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
37 </outputs> |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
38 |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
39 <tests> |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
40 <test> |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
41 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
42 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
43 <param name="rscript_output" value="true" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
44 <output name="outputxls" file="output.junction.xls" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
45 <output name="outputr" file="output.junction_plot.r" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
46 <output name="outputpdf" file="output.splice_events.pdf" compare="sim_size" /> |
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
47 <output name="outputjpdf" file="output.splice_junction.pdf" compare="sim_size" /> |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
48 </test> |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
49 </tests> |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
50 |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
51 <help><![CDATA[ |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
52 junction_annotation.py |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
53 ++++++++++++++++++++++ |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
54 |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
55 For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
56 format, this program will compare detected splice junctions to reference gene model. splicing |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
57 annotation is performed in two levels: splice event level and splice junction level. |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
58 |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
59 * splice event: An RNA read, especially long read, can be spliced 2 or more times, each time is called a splicing event; In this sense, 100 spliced reads can produce >= 100 splicing events. |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
60 * splice junction: multiple splicing events spanning the same intron can be consolidated into one splicing junction. |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
61 |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
62 All detected junctions can be grouped to 3 exclusive categories: |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
63 |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
64 1. Annotated: The junction is part of the gene model. Both splice sites, 5' splice site |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
65 (5'SS) and 3'splice site (3'SS) can be annotated by reference gene model. |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
66 2. complete_novel: Complete new junction. Neither of the two splice sites cannot be annotated by gene model |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
67 3. partial_novel: One of the splice site (5'SS or 3'SS) is new, while the other splice site is annotated (known) |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
68 |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
69 Inputs |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
70 ++++++++++++++ |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
71 |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
72 Input BAM/SAM file |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
73 Alignment file in BAM/SAM format. |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
74 |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
75 Reference gene model |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
76 Gene model in BED format. |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
77 |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
78 Minimum intron length (default=50) |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
79 Minimum intron length (bp). |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
80 |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
81 |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
82 Output |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
83 ++++++++++++++ |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
84 |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
85 1. output.junc.anno.junction.xls: |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
86 - chrom ID |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
87 - start position of junction (coordinate is 0 based) |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
88 - end position of junction (coordinate is 1 based) |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
89 - number of splice events supporting this junction |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
90 - 'annotated', 'complete_novel' or 'partial_novel'. |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
91 2. output.anno.junction_plot.r: R script to generate pie chart |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
92 3. output.splice_junction.pdf: plot of splice junctions |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
93 4. output.splice_events.pdf: plot of splice events |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
94 |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
95 .. image:: $PATH_TO_IMAGES/junction.png |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
96 :height: 400 px |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
97 :width: 850 px |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
98 :scale: 80 % |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
99 |
51
09846d5169fa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
iuc
parents:
49
diff
changeset
|
100 @ABOUT@ |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
101 |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
102 ]]> |
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
103 </help> |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
104 |
49
6b33e31bda10
Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents:
45
diff
changeset
|
105 <expand macro="citations" /> |
45
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
106 |
eb339c5849bb
Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff
changeset
|
107 </tool> |