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comparison inner_distance.xml @ 29:907d4b021ff6

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author nilesh
date Thu, 11 Jul 2013 12:31:33 -0400
parents adc934fb9a76
children cc5eaa9376d8
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28:6e438a559a10 29:907d4b021ff6
1 <tool id="inner_distance" name="Inner Distance">
2 <description>calculate the inner distance (or insert size) between two paired RNA reads</description>
3 <requirements>
4 <requirement type="package" version="2.15.1">R</requirement>
5 <requirement type="package" version="2.3.7">rseqc</requirement>
6 </requirements>
7 <command interpreter="python"> inner_distance.py -i $input -o output -r $refgene
8
9 #if $bounds.hasLowerBound
10 -l $bounds.lowerBound
11 #end if
12
13 #if $bounds2.hasUpperBound
14 -u $bounds2.upperBound
15 #end if
16
17 #if $steps.step
18 -s $steps.stepSize
19 #end if
20 </command>
21 <inputs>
22 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
23 <param name="refgene" type="data" format="bed" label="reference gene model" />
24 <conditional name="bounds">
25 <param name="hasLowerBound" type="boolean" label="Specify lower bound" value="false"/>
26 <when value="true">
27 <param name="lowerBound" type="integer" value="-250" label="Estimated Lower Bound (bp, default=-250)" />
28 </when>
29 </conditional>
30 <conditional name="bounds2">
31 <param name="hasUpperBound" type="boolean" label="Specify upper bound" value="false" />
32 <when value="true">
33 <param name="upperBound" type="integer" value="250" label="Estimated Upper Bound (bp, default=250)" />
34 </when>
35 </conditional>
36 <conditional name="steps">
37 <param name="step" type="boolean" label="Specify step size" value="false" />
38 <when value="true">
39 <param name="stepSize" type="integer" value="5" label="Step size (bp, default=5)" />
40 </when>
41 </conditional>
42 </inputs>
43 <outputs>
44 <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt"/>
45 <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" />
46 <data format="pdf" name="outputpdf" from_work_dir="output.inner_distance_plot.pdf" />
47 <data format="r" name="outputr" from_work_dir="output.inner_distance_plot.r" />
48 </outputs>
49 <help>
50 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
51
52 -----
53
54 About RSeQC
55 +++++++++++
56
57 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.
58
59 The RSeQC package is licensed under the GNU GPL v3 license.
60
61 Inputs
62 ++++++++++++++
63
64 Input BAM/SAM file
65 Alignment file in BAM/SAM format.
66
67 Reference gene model
68 Gene model in BED format.
69
70 Estimated Upper/Lower Bounds (defaults=250 and -250)
71 Estimated upper/lower bounds of inner distance (bp).
72
73 Step size (default=5)
74 Step size of histogram
75
76
77 Output
78 ++++++++++++++
79
80 1. output.inner_distance.txt:
81 - first column is read ID
82 -second column is inner distance. Could be negative value if PE reads were overlapped or mapping error (e.g. Read1_start < Read2_start, while Read1_end >> Read2_end due to spliced mapping of read1)
83 - third column indicates how paired reads were mapped: PE_within_same_exon, PE_within_diff_exon,PE_reads_overlap
84 2. output..inner_distance_freq.txt:
85 - inner distance starts
86 - inner distance ends
87 - number of read pairs
88 - note the first 2 columns are left side half open interval
89 3. output.inner_distance_plot.r: R script to generate histogram
90 4. output.inner_distance_plot.pdf: histogram plot
91
92 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/inner_distance.png
93
94 </help>
95 </tool>