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Reupload tarball (all files were again deleted by toolshed).
author lparsons
date Wed, 23 Jul 2014 10:44:50 -0400
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39:1b769e35cd8e 40:1e66f05a23aa
1 <tool id="rseqc_RPKM_count" name="RPKM Count" version="2.3.9">
2 <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>
3 <requirements>
4 <requirement type="package" version="1.7.1">numpy</requirement>
5 <requirement type="package" version="2.3.9">rseqc</requirement>
6 </requirements>
7 <command>
8 ln -s "${input}" "local_input.bam" &amp;&amp;
9 ln -s "${input.metadata.bam_index}" "local_input.bam.bai" &amp;&amp;
10 RPKM_count.py -i "local_input.bam" -o output -r $refgene
11
12 #if str($strand_type.strand_specific) == "pair"
13 -d
14 #if str($strand_type.pair_type) == "sd"
15 '1++,1--,2+-,2-+'
16 #else
17 '1+-,1-+,2++,2--'
18 #end if
19 #end if
20
21 #if str($strand_type.strand_specific) == "single"
22 -d
23 #if str($strand_type.single_type) == "s"
24 '++,--'
25 #else
26 '+-,-+'
27 #end if
28 #end if
29
30 #if $skiphits
31 -u
32 #end if
33
34 #if $onlyexonic
35 -e
36 #end if
37
38 </command>
39 <stdio>
40 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
41 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
42 </stdio>
43 <inputs>
44 <param name="input" type="data" format="bam" label="input bam/sam file" />
45 <param name="refgene" type="data" format="bed" label="Reference gene model" />
46 <conditional name="strand_type">
47 <param name="strand_specific" type="select" label="Strand-specific?" value="None">
48 <option value="none">None</option>
49 <option value="pair">Pair-End RNA-seq</option>
50 <option value="single">Single-End RNA-seq</option>
51 </param>
52 <when value="pair">
53 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd">
54 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
55 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
56 </param>
57 </when>
58 <when value="single">
59 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s">
60 <option value="s">positive --> positive; negative --> negative</option>
61 <option value="d">positive --> negative; negative --> positive</option>
62 </param>
63 </when>
64 <when value="none"></when>
65 </conditional>
66 <param name="skiphits" type="boolean" value="false" label="Skip Multiple Hit Reads" />
67 <param name="onlyexonic" type="boolean" value="false" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" />
68 </inputs>
69 <outputs>
70 <data format="xls" name="outputxls" from_work_dir="output_read_count.xls"/>
71 </outputs>
72 <help>
73 RPKM_count.py
74 +++++++++++++
75
76 Given a BAM file and reference gene model, this program will calculate the raw count and RPKM
77 values for transcript at exon, intron and mRNA level. For strand specific RNA-seq data,
78 program will assign read to its parental gene according to strand rule, if you don't know the
79 strand rule, run infer_experiment.py. Please note that chromosome ID, genome cooridinates
80 should be concordant between BAM and BED files.
81
82 Inputs
83 ++++++++++++++
84
85 Input BAM/SAM file
86 Alignment file in BAM/SAM format.
87
88 Reference gene model
89 Gene model in BED format.
90
91 Strand sequencing type (default=none)
92 See Infer Experiment tool if uncertain.
93
94 Options
95 ++++++++++++++
96
97 Skip Multiple Hit Reads
98 Use Multiple hit reads or use only uniquely mapped reads.
99
100 Only use exonic reads
101 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads.
102
103 Sample Output
104 ++++++++++++++
105
106 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
107 chrom start end accession score gene strand tag count (+) tag count (-) RPKM (+) RPKM (-)
108 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
109 chr1 29213722 29313959 NM_001166007_intron_1 0 '+' 431 4329 0.086 0.863
110 chr1 29314417 29319841 NM_001166007_intron_2 0 '+' 31 1 0.114 0.004
111 chr1 29320054 29323726 NM_001166007_intron_3 0 '+' 32 0 0.174 0.000
112 chr1 29213602 29213722 NM_001166007_exon_1 0 '+' 164 0 27.321 0.000
113 chr1 29313959 29314417 NM_001166007_exon_2 0 '+' 1699 4 74.158 0.175
114 chr1 29319841 29320054 NM_001166007_exon_3 0 '+' 528 1 49.554 0.094
115 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
116
117 -----
118
119 About RSeQC
120 +++++++++++
121
122 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.
123
124 The RSeQC package is licensed under the GNU GPL v3 license.
125
126 .. image:: http://rseqc.sourceforge.net/_static/logo.png
127
128 .. _RSeQC: http://rseqc.sourceforge.net/
129
130
131 </help>
132 </tool>