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comparison RPKM_count.xml @ 1:8dab2cfd456f default tip

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author nilesh
date Thu, 18 Jul 2013 11:24:42 -0500
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0:0e4ef5fef2c5 1:8dab2cfd456f
1 <tool id="RPKM_count" name="RPKM Count">
2 <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>
3 <requirements>
4 <requirement type="package" version="0.1.18">samtools</requirement>
5 <requirement type="package" version="2.3.7">rseqc</requirement>
6 </requirements>
7 <command interpreter="python"> samtoolshelper.py RPKM_count.py -i $input -o output -r $refgene
8
9 #if $nx
10 -x
11 #end if
12
13 #if str($strand_type.strand_specific) == "pair"
14 -d
15 #if str($strand_type.pair_type) == "sd"
16 '1++,1--,2+-,2-+'
17 #else
18 '1+-,1-+,2++,2--'
19 #end if
20 #end if
21
22 #if str($strand_type.strand_specific) == "single"
23 -d
24 #if str($strand_type.single_type) == "s"
25 '++,--'
26 #else
27 '+-,-+'
28 #end if
29 #end if
30
31 #if $skiphits
32 -u
33 #end if
34
35 #if $onlyexonic
36 -e
37 #end if
38
39 </command>
40 <inputs>
41 <param name="input" type="data" format="bam" label="input bam/sam file" />
42 <param name="refgene" type="data" format="bed" label="Reference gene model" />
43 <conditional name="strand_type">
44 <param name="strand_specific" type="select" label="Strand-specific?" value="None">
45 <option value="none">None</option>
46 <option value="pair">Pair-End RNA-seq</option>
47 <option value="single">Single-End RNA-seq</option>
48 </param>
49 <when value="pair">
50 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd">
51 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
52 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
53 </param>
54 </when>
55 <when value="single">
56 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s">
57 <option value="s">positive --> positive; negative --> negative</option>
58 <option value="d">positive --> negative; negative --> positive</option>
59 </param>
60 </when>
61 <when value="none"></when>
62 </conditional>
63 <param name="skiphits" type="boolean" value="false" label="Skip Multiple Hit Reads" />
64 <param name="onlyexonic" type="boolean" value="false" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" />
65 </inputs>
66 <outputs>
67 <data format="xls" name="outputxls" from_work_dir="output_read_count.xls"/>
68 </outputs>
69 <tests>
70 <test>
71 <param name="input" value="Pairend_nonStrandSpecific_36mer_Human_hg19.bam" />
72 <param name="refgene" value="hg19_RefSeq.bed" />
73 <output name="outputxls" file="rpkmctout_read_count.xls" />
74 </test>
75 </tests>
76 <help>
77 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
78
79 -----
80
81 About RSeQC
82 +++++++++++
83
84 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.
85
86 The RSeQC package is licensed under the GNU GPL v3 license.
87
88 Inputs
89 ++++++++++++++
90
91 Input BAM/SAM file
92 Alignment file in BAM/SAM format.
93
94 Reference gene model
95 Gene model in BED format.
96
97 Strand sequencing type (default=none)
98 See Infer Experiment tool if uncertain.
99
100 Options
101 ++++++++++++++
102
103 Skip Multiple Hit Reads
104 Use Multiple hit reads or use only uniquely mapped reads.
105
106 Only use exonic reads
107 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads.
108
109 </help>
110 </tool>