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comparison FPKM_count.xml @ 3:71ed55a3515a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:22:57 -0400
parents
children 017eaaf58e5e
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2:ebadf9ee2d08 3:71ed55a3515a
1 <tool id="rseqc_FPKM_count" name="FPKM Count" version="@WRAPPER_VERSION@">
2 <description>calculates raw read count, FPM, and FPKM for each gene</description>
3
4 <macros>
5 <import>rseqc_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements" />
9
10 <expand macro="stdio" />
11
12 <version_command><![CDATA[FPKM_count.py --version]]></version_command>
13
14 <command><![CDATA[
15 ln -sf '${input}' 'local_input.bam' &&
16 ln -sf '${input.metadata.bam_index}' 'local_input.bam.bai' &&
17 FPKM_count.py -i 'local_input.bam' -o output -r '${refgene}'
18
19 #if str($strand_type.strand_specific) == "pair"
20 -d
21 #if str($strand_type.pair_type) == "sd"
22 '1++,1--,2+-,2-+'
23 #else
24 '1+-,1-+,2++,2--'
25 #end if
26 #end if
27
28 #if str($strand_type.strand_specific) == "single"
29 -d
30 #if str($strand_type.single_type) == "s"
31 '++,--'
32 #else
33 '+-,-+'
34 #end if
35 #end if
36
37 @MULTIHITS@
38
39 $onlyexonic
40 --single-read="${singleread}"
41 ]]>
42 </command>
43
44 <inputs>
45 <expand macro="bam_param" />
46 <expand macro="refgene_param" />
47 <expand macro="strand_type_param" />
48 <expand macro="multihits_param" />
49 <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)"/>
50 <param name="singleread" type="select" label="How should read-pairs that only have one end mapped be counted?" help="(--single-read)">
51 <option value="1" selected="true">Treat it as a whole fragment (1)</option>
52 <option value="0.5">Treat it as a half fragment (0.5)</option>
53 <option value="0">Ignore it (0)</option>
54 </param>
55 </inputs>
56
57 <outputs>
58 <data format="xls" name="outputxls" from_work_dir="output.FPKM.xls"/>
59 </outputs>
60
61 <tests>
62 <test>
63 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
64 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
65 <output name="outputxls" file="output.FPKM.xls"/>
66 </test>
67 </tests>
68
69 <help><![CDATA[
70 FPKM_count.py
71 +++++++++++++
72
73 Given a BAM file and reference gene model, this program will calculate the raw
74 read count, FPM (fragments per million), and FPKM (fragments per million
75 mapped reads per kilobase exon) for each gene in a BED file. For strand
76 specific RNA-seq data, program will assign read to its parental gene according
77 to strand rule, if you don't know the strand rule, run infer_experiment.py.
78 Please note that chromosome ID, genome cooridinates should be concordant
79 between BAM and BED files.
80
81 Inputs
82 ++++++++++++++
83
84 Input BAM/SAM file
85 Alignment file in BAM/SAM format.
86
87 Reference gene model
88 Gene model in BED format.
89
90 Strand sequencing type (default=none)
91 See Infer Experiment tool if uncertain.
92
93 Options
94 ++++++++++++++
95
96 Skip Multiple Hit Reads
97 Use Multiple hit reads or use only uniquely mapped reads.
98
99 Minimum mapping quality
100 Minimum mapping quality (phred scaled) for an alignment to be called
101 "uniquely mapped". default=30
102
103 Only use exonic reads
104 Renders program only used exonic (UTR exons and CDS exons) reads,
105 otherwise use all reads.
106
107 Single Reads
108 How to count read-pairs that only have one end mapped. 0: ignore it. 0.5:
109 treat it as half fragment. 1: treat it as whole fragment. default=1
110
111 Sample Output
112 ++++++++++++++
113
114 ====== ========= ========= ========= ========= =========== ========== ============ ============
115 #chrom st end accession mRNA_size gene_strand Frag_count FPM FPKM
116 ====== ========= ========= ========= ========= =========== ========== ============ ============
117 chr1 100652477 100715409 NM_001918 10815.0 ‘-‘ 5498.0 191.73788949 17.728884835
118 chr1 175913961 176176380 NM_022457 2789.0 ‘-‘ 923.0 32.188809021 11.541344217
119 chr1 150980972 151008189 NM_021222 2977.0 ‘+’ 687.0 23.958517657 8.0478729115
120 chr1 6281252 6296044 NM_012405 4815.0 ‘-‘ 1396.0 48.684265866 10.11095864
121 chr1 20959947 20978004 NM_032409 2660.0 ‘+’ 509.0 17.750925018 6.6732800821
122 chr1 32479294 32509482 NM_006559 2891.0 ‘+’ 2151.0 75.014223408 25.947500314
123 ====== ========= ========= ========= ========= =========== ========== ============ ============
124
125 @ABOUT@
126
127 ]]>
128 </help>
129
130 <expand macro="citations" />
131
132 </tool>