Mercurial > repos > nilesh > rseqc

annotate RPKM_count.xml @ 50:f242ee103277 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
author lparsons
date Tue, 03 May 2016 16:36:57 -0400
parents 6b33e31bda10
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
1 <tool id="rseqc_RPKM_count" name="RPKM Count" version="2.4galaxy1">
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
2 <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</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
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
8 <requirements>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
9 <expand macro="requirement_package_numpy" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
10 <expand macro="requirement_package_rseqc" />
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
11 </requirements>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
12
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
13 <expand macro="stdio" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
14
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
15 <version_command><![CDATA[RPKM_count.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
16
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
17 <command><![CDATA[
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
18 ln -s "${input}" "local_input.bam" &&
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
19 ln -s "${input.metadata.bam_index}" "local_input.bam.bai" &&
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
20 RPKM_count.py -i "local_input.bam" -o output -r $refgene
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
21
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
22 #if str($strand_type.strand_specific) == "pair"
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
23 -d
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
24 #if str($strand_type.pair_type) == "sd"
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
25 '1++,1--,2+-,2-+'
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
26 #else
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
27 '1+-,1-+,2++,2--'
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
28 #end if
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
29 #end if
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
30
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
31 #if str($strand_type.strand_specific) == "single"
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
32 -d
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
33 #if str($strand_type.single_type) == "s"
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
34 '++,--'
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
35 #else
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
36 '+-,-+'
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
37 #end if
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
38 #end if
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
39
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
40 #if $multihits.skipmultihits
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
41 --skip-multi-hits
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
42 --mapq=$multihits.mapq
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
43 #end if
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
44
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
45 $onlyexonic
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
46 ]]>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
47 </command>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
48
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
49 <inputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
50 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
51 <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
52 <conditional name="strand_type">
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
53 <param name="strand_specific" type="select" label="Strand-specific?" value="None">
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
54 <option value="none">None</option>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
55 <option value="pair">Pair-End RNA-seq</option>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
56 <option value="single">Single-End RNA-seq</option>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
57 </param>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
58 <when value="pair">
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
59 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd" help="(--strand)">
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
60 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
61 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
62 </param>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
63 </when>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
64 <when value="single">
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
65 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s" help="(--strand)">
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
66 <option value="s">positive --> positive; negative --> negative</option>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
67 <option value="d">positive --> negative; negative --> positive</option>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
68 </param>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
69 </when>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
70 <when value="none"></when>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
71 </conditional>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
72
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
73 <conditional name="multihits">
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
74 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" help="(--skip-multi-hits)" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
75 <when value="true">
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
76 <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
77 </when>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
78 <when value="false" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
79 </conditional>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
80
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
81 <param name="onlyexonic" type="boolean" value="false" truevalue="--only-exonic" falsevalue="" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" help="(--only-exonic)"/>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
82 </inputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
83
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
84 <outputs>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
85 <data format="xls" name="outputxls" from_work_dir="output_read_count.xls"/>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
86 </outputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
87
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
88 <tests>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
89 <test>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
90 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
91 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
92 <output name="outputxls" file="output_read_count.xls"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
93 </test>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
94 </tests>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
95
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
96 <help><![CDATA[
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
97 RPKM_count.py
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
98 +++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
99
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
100 Given a BAM file and reference gene model, this program will calculate the raw count and RPKM
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
101 values for transcript at exon, intron and mRNA level. For strand specific RNA-seq data,
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
102 program will assign read to its parental gene according to strand rule, if you don't know the
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
103 strand rule, run infer_experiment.py. Please note that chromosome ID, genome cooridinates
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
104 should be concordant between BAM and BED files.
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
105
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
106 Inputs
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
107 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
108
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
109 Input BAM/SAM file
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
110 Alignment file in BAM/SAM format.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
111
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
112 Reference gene model
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
113 Gene model in BED format.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
114
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
115 Strand sequencing type (default=none)
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
116 See Infer Experiment tool if uncertain.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
117
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
118 Options
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
119 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
120
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
121 Skip Multiple Hit Reads
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
122 Use Multiple hit reads or use only uniquely mapped reads.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
123
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
124 Only use exonic reads
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
125 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
126
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
127 Sample Output
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
128 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
129
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
130 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
131 chrom start end accession score gene strand tag count (+) tag count (-) RPKM (+) RPKM (-)
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
132 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
133 chr1 29213722 29313959 NM_001166007_intron_1 0 '+' 431 4329 0.086 0.863
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
134 chr1 29314417 29319841 NM_001166007_intron_2 0 '+' 31 1 0.114 0.004
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
135 chr1 29320054 29323726 NM_001166007_intron_3 0 '+' 32 0 0.174 0.000
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
136 chr1 29213602 29213722 NM_001166007_exon_1 0 '+' 164 0 27.321 0.000
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
137 chr1 29313959 29314417 NM_001166007_exon_2 0 '+' 1699 4 74.158 0.175
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
138 chr1 29319841 29320054 NM_001166007_exon_3 0 '+' 528 1 49.554 0.094
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
139 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
140
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
141 -----
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
142
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
143 About RSeQC
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
144 +++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
145
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
146 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
147
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
148 The RSeQC package is licensed under the GNU GPL v3 license.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
149
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
150 .. image:: http://rseqc.sourceforge.net/_static/logo.png
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
151
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
152 .. _RSeQC: http://rseqc.sourceforge.net/
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
153 ]]>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
154 </help>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
155
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
156 <expand macro="citations" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
157
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
158 </tool>