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comparison RPKM_count.xml @ 49:6b33e31bda10 draft

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Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
author lparsons
date Thu, 16 Jul 2015 17:43:43 -0400
parents eb339c5849bb
children
comparison
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48:2e6190c29c54 49:6b33e31bda10
1 <tool id="rseqc_RPKM_count" name="RPKM Count" version="2.4"> 1 <tool id="rseqc_RPKM_count" name="RPKM Count" version="2.4galaxy1">
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
4 <macros>
5 <import>rseqc_macros.xml</import>
6 </macros>
7
3 <requirements> 8 <requirements>
4 <requirement type="package" version="1.7.1">numpy</requirement> 9 <expand macro="requirement_package_numpy" />
5 <requirement type="package" version="2.4">rseqc</requirement> 10 <expand macro="requirement_package_rseqc" />
6 </requirements> 11 </requirements>
7 <command> 12
8 ln -s "${input}" "local_input.bam" &amp;&amp; 13 <expand macro="stdio" />
9 ln -s "${input.metadata.bam_index}" "local_input.bam.bai" &amp;&amp; 14
15 <version_command><![CDATA[RPKM_count.py --version]]></version_command>
16
17 <command><![CDATA[
18 ln -s "${input}" "local_input.bam" &&
19 ln -s "${input.metadata.bam_index}" "local_input.bam.bai" &&
10 RPKM_count.py -i "local_input.bam" -o output -r $refgene 20 RPKM_count.py -i "local_input.bam" -o output -r $refgene
11 21
12 #if str($strand_type.strand_specific) == "pair" 22 #if str($strand_type.strand_specific) == "pair"
13 -d 23 -d
14 #if str($strand_type.pair_type) == "sd" 24 #if str($strand_type.pair_type) == "sd"
25 #else 35 #else
26 '+-,-+' 36 '+-,-+'
27 #end if 37 #end if
28 #end if 38 #end if
29 39
30 #if $skiphits 40 #if $multihits.skipmultihits
31 -u 41 --skip-multi-hits
42 --mapq=$multihits.mapq
32 #end if 43 #end if
33 44
34 #if $onlyexonic 45 $onlyexonic
35 -e 46 ]]>
36 #end if 47 </command>
37 48
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> 49 <inputs>
44 <param name="input" type="data" format="bam" label="input bam/sam file" /> 50 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
45 <param name="refgene" type="data" format="bed" label="Reference gene model" /> 51 <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
46 <conditional name="strand_type"> 52 <conditional name="strand_type">
47 <param name="strand_specific" type="select" label="Strand-specific?" value="None"> 53 <param name="strand_specific" type="select" label="Strand-specific?" value="None">
48 <option value="none">None</option> 54 <option value="none">None</option>
49 <option value="pair">Pair-End RNA-seq</option> 55 <option value="pair">Pair-End RNA-seq</option>
50 <option value="single">Single-End RNA-seq</option> 56 <option value="single">Single-End RNA-seq</option>
51 </param> 57 </param>
52 <when value="pair"> 58 <when value="pair">
53 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd"> 59 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd" help="(--strand)">
54 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option> 60 <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> 61 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
56 </param> 62 </param>
57 </when> 63 </when>
58 <when value="single"> 64 <when value="single">
59 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s"> 65 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s" help="(--strand)">
60 <option value="s">positive --> positive; negative --> negative</option> 66 <option value="s">positive --> positive; negative --> negative</option>
61 <option value="d">positive --> negative; negative --> positive</option> 67 <option value="d">positive --> negative; negative --> positive</option>
62 </param> 68 </param>
63 </when> 69 </when>
64 <when value="none"></when> 70 <when value="none"></when>
65 </conditional> 71 </conditional>
66 <param name="skiphits" type="boolean" value="false" label="Skip Multiple Hit Reads" /> 72
67 <param name="onlyexonic" type="boolean" value="false" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" /> 73 <conditional name="multihits">
74 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" help="(--skip-multi-hits)" />
75 <when value="true">
76 <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" />
77 </when>
78 <when value="false" />
79 </conditional>
80
81 <param name="onlyexonic" type="boolean" value="false" truevalue="--only-exonic" falsevalue="" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" help="(--only-exonic)"/>
68 </inputs> 82 </inputs>
83
69 <outputs> 84 <outputs>
70 <data format="xls" name="outputxls" from_work_dir="output_read_count.xls"/> 85 <data format="xls" name="outputxls" from_work_dir="output_read_count.xls"/>
71 </outputs> 86 </outputs>
72 <help> 87
88 <tests>
89 <test>
90 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
91 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
92 <output name="outputxls" file="output_read_count.xls"/>
93 </test>
94 </tests>
95
96 <help><![CDATA[
73 RPKM_count.py 97 RPKM_count.py
74 +++++++++++++ 98 +++++++++++++
75 99
76 Given a BAM file and reference gene model, this program will calculate the raw count and RPKM 100 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, 101 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 102 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 103 strand rule, run infer_experiment.py. Please note that chromosome ID, genome cooridinates
80 should be concordant between BAM and BED files. 104 should be concordant between BAM and BED files.
81 105
82 Inputs 106 Inputs
83 ++++++++++++++ 107 ++++++++++++++
84 108
85 Input BAM/SAM file 109 Input BAM/SAM file
95 ++++++++++++++ 119 ++++++++++++++
96 120
97 Skip Multiple Hit Reads 121 Skip Multiple Hit Reads
98 Use Multiple hit reads or use only uniquely mapped reads. 122 Use Multiple hit reads or use only uniquely mapped reads.
99 123
100 Only use exonic reads 124 Only use exonic reads
101 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads. 125 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads.
102 126
103 Sample Output 127 Sample Output
104 ++++++++++++++ 128 ++++++++++++++
105 129
111 chr1 29320054 29323726 NM_001166007_intron_3 0 '+' 32 0 0.174 0.000 135 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 0.000 136 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 0.175 137 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 0.094 138 chr1 29319841 29320054 NM_001166007_exon_3 0 '+' 528 1 49.554 0.094
115 ===== ======== ======== ===================== ===== =========== ============= ============= ======== ========= 139 ===== ======== ======== ===================== ===== =========== ============= ============= ======== =========
116 140
117 ----- 141 -----
118 142
119 About RSeQC 143 About RSeQC
120 +++++++++++ 144 +++++++++++
121 145
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. 146 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.
123 147
124 The RSeQC package is licensed under the GNU GPL v3 license. 148 The RSeQC package is licensed under the GNU GPL v3 license.
125 149
126 .. image:: http://rseqc.sourceforge.net/_static/logo.png 150 .. image:: http://rseqc.sourceforge.net/_static/logo.png
127 151
128 .. _RSeQC: http://rseqc.sourceforge.net/ 152 .. _RSeQC: http://rseqc.sourceforge.net/
153 ]]>
154 </help>
129 155
156 <expand macro="citations" />
130 157
131 </help>
132 </tool> 158 </tool>