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comparison inner_distance.xml @ 48:2e6190c29c54 draft

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author lparsons
date Tue, 21 Apr 2015 10:27:06 -0400
parents eb339c5849bb
children 6b33e31bda10
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47:10d30c88fe05 48:2e6190c29c54
1 <tool id="rseqc_inner_distance" name="Inner Distance" version="2.4">
2 <description>calculate the inner distance (or insert size) between two paired RNA reads</description>
3 <requirements>
4 <requirement type="package" version="3.0.3">R</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement>
6 <requirement type="package" version="2.4">rseqc</requirement>
7 </requirements>
8 <command>
9 inner_distance.py -i $input -o output -r $refgene
10
11 #if $bounds.hasLowerBound
12 -l $bounds.lowerBound
13 #end if
14
15 #if $bounds2.hasUpperBound
16 -u $bounds2.upperBound
17 #end if
18
19 #if $steps.step
20 -s $steps.stepSize
21 #end if
22 </command>
23 <stdio>
24 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
25 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
26 </stdio>
27 <inputs>
28 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
29 <param name="refgene" type="data" format="bed" label="reference gene model" />
30 <conditional name="bounds">
31 <param name="hasLowerBound" type="boolean" label="Specify lower bound" value="false"/>
32 <when value="true">
33 <param name="lowerBound" type="integer" value="-250" label="Estimated Lower Bound (bp, default=-250)" />
34 </when>
35 </conditional>
36 <conditional name="bounds2">
37 <param name="hasUpperBound" type="boolean" label="Specify upper bound" value="false" />
38 <when value="true">
39 <param name="upperBound" type="integer" value="250" label="Estimated Upper Bound (bp, default=250)" />
40 </when>
41 </conditional>
42 <conditional name="steps">
43 <param name="step" type="boolean" label="Specify step size" value="false" />
44 <when value="true">
45 <param name="stepSize" type="integer" value="5" label="Step size (bp, default=5)" />
46 </when>
47 </conditional>
48 </inputs>
49 <outputs>
50 <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string} (Text)"/>
51 <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string} (Freq Text)" />
52 <data format="pdf" name="outputpdf" from_work_dir="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
53 <data format="txt" name="outputr" from_work_dir="output.inner_distance_plot.r" label="${tool.name} on ${on_string} (R Script)" />
54 </outputs>
55 <help>
56 inner_distance.py
57 +++++++++++++++++
58
59 This module is used to calculate the inner distance (or insert size) between two paired RNA
60 reads. The distance is the mRNA length between two paired fragments. We first determine the
61 genomic (DNA) size between two paired reads: D_size = read2_start - read1_end, then
62
63 * if two paired reads map to the same exon: inner distance = D_size
64 * if two paired reads map to different exons:inner distance = D_size - intron_size
65 * if two paired reads map non-exonic region (such as intron and intergenic region): inner distance = D_size
66 * The inner_distance might be a negative value if two fragments were overlapped.
67
68 NOTE: Not all read pairs were used to estimate the inner distance distribution. Those low
69 quality, PCR duplication, multiple mapped reads were skipped.
70
71 Inputs
72 ++++++++++++++
73
74 Input BAM/SAM file
75 Alignment file in BAM/SAM format.
76
77 Reference gene model
78 Gene model in BED format.
79
80 Estimated Upper/Lower Bounds (defaults=250 and -250)
81 Estimated upper/lower bounds of inner distance (bp).
82
83 Step size (default=5)
84 Step size of histogram
85
86
87 Output
88 ++++++++++++++
89
90 1. output.inner_distance.txt:
91 - first column is read ID
92 -second column is inner distance. Could be negative value if PE reads were overlapped or mapping error (e.g. Read1_start &lt; Read2_start, while Read1_end >> Read2_end due to spliced mapping of read1)
93 - third column indicates how paired reads were mapped: PE_within_same_exon, PE_within_diff_exon,PE_reads_overlap
94 2. output..inner_distance_freq.txt:
95 - inner distance starts
96 - inner distance ends
97 - number of read pairs
98 - note the first 2 columns are left side half open interval
99 3. output.inner_distance_plot.r: R script to generate histogram
100 4. output.inner_distance_plot.pdf: histogram plot
101
102 .. image:: http://rseqc.sourceforge.net/_images/inner_distance.png
103 :height: 600 px
104 :width: 600 px
105 :scale: 80 %
106
107
108 -----
109
110 About RSeQC
111 +++++++++++
112
113 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.
114
115 The RSeQC package is licensed under the GNU GPL v3 license.
116
117 .. image:: http://rseqc.sourceforge.net/_static/logo.png
118
119 .. _RSeQC: http://rseqc.sourceforge.net/
120
121
122 </help>
123 </tool>