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comparison RPKM_count.xml @ 32:580ee0c4bc4e

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Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
author lparsons
date Mon, 07 Oct 2013 15:01:13 -0400
parents cc5eaa9376d8
children
comparison
equal deleted inserted replaced
31:cc5eaa9376d8 32:580ee0c4bc4e
1 <tool id="RPKM_count" name="RPKM Count" version="1.1"> 1 <tool id="rseqc_RPKM_count" name="RPKM Count" version="1.1">
2 <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description> 2 <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.7.1">numpy</requirement> 4 <requirement type="package" version="1.7.1">numpy</requirement>
5 <requirement type="package" version="2.3.7">rseqc</requirement> 5 <requirement type="package" version="2.3.7">rseqc</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 ln -s "${input}" "local_input.bam" &amp;&amp; 8 ln -s "${input}" "local_input.bam" &amp;&amp;
9 ln -s "${input.metadata.bam_index}" "local_input.bam.bai" &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 10 RPKM_count.py -i "local_input.bam" -o output -r $refgene
11 11
12 #if str($strand_type.strand_specific) == "pair" 12 #if str($strand_type.strand_specific) == "pair"
13 -d 13 -d
14 #if str($strand_type.pair_type) == "sd" 14 #if str($strand_type.pair_type) == "sd"
15 '1++,1--,2+-,2-+' 15 '1++,1--,2+-,2-+'
16 #else 16 #else
17 '1+-,1-+,2++,2--' 17 '1+-,1-+,2++,2--'
18 #end if 18 #end if
19 #end if 19 #end if
20 20
21 #if str($strand_type.strand_specific) == "single" 21 #if str($strand_type.strand_specific) == "single"
22 -d 22 -d
23 #if str($strand_type.single_type) == "s" 23 #if str($strand_type.single_type) == "s"
24 '++,--' 24 '++,--'
25 #else 25 #else
26 '+-,-+' 26 '+-,-+'
27 #end if 27 #end if
28 #end if 28 #end if
29 29
30 #if $skiphits 30 #if $skiphits
31 -u 31 -u
32 #end if 32 #end if
33 33
34 #if $onlyexonic 34 #if $onlyexonic
35 -e 35 -e
36 #end if 36 #end if
37 37
38 </command> 38 </command>
39 <inputs>
40 <param name="input" type="data" format="bam" label="input bam/sam file" />
41 <param name="refgene" type="data" format="bed" label="Reference gene model" />
42 <conditional name="strand_type">
43 <param name="strand_specific" type="select" label="Strand-specific?" value="None">
44 <option value="none">None</option>
45 <option value="pair">Pair-End RNA-seq</option>
46 <option value="single">Single-End RNA-seq</option>
47 </param>
48 <when value="pair">
49 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd">
50 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
51 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
52 </param>
53 </when>
54 <when value="single">
55 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s">
56 <option value="s">positive --> positive; negative --> negative</option>
57 <option value="d">positive --> negative; negative --> positive</option>
58 </param>
59 </when>
60 <when value="none"></when>
61 </conditional>
62 <param name="skiphits" type="boolean" value="false" label="Skip Multiple Hit Reads" />
63 <param name="onlyexonic" type="boolean" value="false" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" />
64 </inputs>
65 <outputs>
66 <data format="xls" name="outputxls" from_work_dir="output_read_count.xls"/>
67 </outputs>
68 <stdio> 39 <stdio>
69 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 40 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
70 <regex match="[Ee]rror" source="both" 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" />
71 </stdio> 42 </stdio>
72 <help> 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 73 RPKM_count.py
74 +++++++++++++ 74 +++++++++++++
75 75
76 Given a BAM file and reference gene model, this program will calculate the raw count and RPKM 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, 77 values for transcript at exon, intron and mRNA level. For strand specific RNA-seq data,
81 81
82 Inputs 82 Inputs
83 ++++++++++++++ 83 ++++++++++++++
84 84
85 Input BAM/SAM file 85 Input BAM/SAM file
86 Alignment file in BAM/SAM format. 86 Alignment file in BAM/SAM format.
87 87
88 Reference gene model 88 Reference gene model
89 Gene model in BED format. 89 Gene model in BED format.
90 90
91 Strand sequencing type (default=none) 91 Strand sequencing type (default=none)
92 See Infer Experiment tool if uncertain. 92 See Infer Experiment tool if uncertain.
93 93
94 Options 94 Options
95 ++++++++++++++ 95 ++++++++++++++
96 96
97 Skip Multiple Hit Reads 97 Skip Multiple Hit Reads
98 Use Multiple hit reads or use only uniquely mapped reads. 98 Use Multiple hit reads or use only uniquely mapped reads.
99 99
100 Only use exonic reads 100 Only use exonic reads
101 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads. 101 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads.
102 102
103 Sample Output 103 Sample Output
104 ++++++++++++++ 104 ++++++++++++++
105 105
106 ===== ======== ======== ===================== ===== =========== ============= ============= ======== ========= 106 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
111 chr1 29320054 29323726 NM_001166007_intron_3 0 '+' 32 0 0.174 0.000 111 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 0.000 112 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 0.175 113 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 0.094 114 chr1 29319841 29320054 NM_001166007_exon_3 0 '+' 528 1 49.554 0.094
115 ===== ======== ======== ===================== ===== =========== ============= ============= ======== ========= 115 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
116 116
117 ----- 117 -----
118 118
119 About RSeQC 119 About RSeQC
120 +++++++++++ 120 +++++++++++
121 121
126 .. image:: http://rseqc.sourceforge.net/_static/logo.png 126 .. image:: http://rseqc.sourceforge.net/_static/logo.png
127 127
128 .. _RSeQC: http://rseqc.sourceforge.net/ 128 .. _RSeQC: http://rseqc.sourceforge.net/
129 129
130 130
131 </help> 131 </help>
132 </tool> 132 </tool>