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comparison bam_stat.xml @ 51:09846d5169fa 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 10:23:21 -0400
parents 6b33e31bda10
children dbedfc5f5a3c
comparison
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50:f242ee103277 51:09846d5169fa
1 <tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="2.4galaxy1"> 1 <tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="@WRAPPER_VERSION@">
2 <description> 2 <description>
3 reads mapping statistics for a provided BAM or SAM file. 3 reads mapping statistics for a provided BAM or SAM file.
4 </description> 4 </description>
5 5
6 <macros> 6 <macros>
7 <import>rseqc_macros.xml</import> 7 <import>rseqc_macros.xml</import>
8 </macros> 8 </macros>
9 9
10 <requirements> 10 <expand macro="requirements" />
11 <expand macro="requirement_package_numpy" />
12 <expand macro="requirement_package_rseqc" />
13 </requirements>
14 11
15 <expand macro="stdio" /> 12 <expand macro="stdio" />
16 13
17 <version_command><![CDATA[bam_stat.py --version]]></version_command> 14 <version_command><![CDATA[bam_stat.py --version]]></version_command>
18 15
19 <command><![CDATA[ 16 <command><![CDATA[
20 bam_stat.py -i $input -q $mapq 2> $output 17 bam_stat.py -i '${input}' -q ${mapq} > '${output}'
21 ]]> 18 ]]>
22 </command> 19 </command>
23 20
24 <inputs> 21 <inputs>
25 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/> 22 <expand macro="bam_param" />
26 <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" /> 23 <expand macro="mapq_param" />
27 </inputs> 24 </inputs>
28 25
29 <outputs> 26 <outputs>
30 <data format="txt" name="output" /> 27 <data format="txt" name="output" />
31 </outputs> 28 </outputs>
32 29
33 <tests> 30 <tests>
34 <test> 31 <test>
35 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 32 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
36 <output name="output" file="bamstats.txt"/> 33 <output name="output" file="output.bamstats.txt" />
37 </test> 34 </test>
38 </tests> 35 </tests>
39 36
40 <help><![CDATA[ 37 <help><![CDATA[
41 bam_stat.py 38 bam_stat.py
50 47
51 Inputs 48 Inputs
52 ++++++++++++++ 49 ++++++++++++++
53 50
54 Input BAM/SAM file 51 Input BAM/SAM file
55 Alignment file in BAM/SAM format. 52 Alignment file in BAM/SAM format.
56 53
57 Minimum mapping quality 54 Minimum mapping quality
58 Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30) 55 Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)
59 56
60 Output 57 Output
61 ++++++++++++++ 58 ++++++++++++++
62 59
63 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped} 60 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}
64 - Uniquely mapped Reads = {read-1} + {read-2} (if paired end) 61 - Uniquely mapped Reads = {read-1} + {read-2} (if paired end)
65 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'} 62 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
66 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads} 63 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads}
67 64
68 ----- 65 @ABOUT@
69
70 About RSeQC
71 +++++++++++
72
73
74 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.
75
76 The RSeQC package is licensed under the GNU GPL v3 license.
77
78 .. image:: http://rseqc.sourceforge.net/_static/logo.png
79
80 .. _RSeQC: http://rseqc.sourceforge.net/
81 66
82 ]]> 67 ]]>
83 </help> 68 </help>
84 69
85 <expand macro="citations" /> 70 <expand macro="citations" />