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comparison read_distribution.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 5873cd7afb67
comparison
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50:f242ee103277 51:09846d5169fa
1 <tool id="rseqc_read_distribution" name="Read Distribution" version="2.4galaxy1"> 1 <tool id="rseqc_read_distribution" name="Read Distribution" version="@WRAPPER_VERSION@">
2 <description>calculates how mapped reads were distributed over genome feature</description> 2 <description>calculates how mapped reads were distributed over genome feature</description>
3 3
4 <macros> 4 <macros>
5 <import>rseqc_macros.xml</import> 5 <import>rseqc_macros.xml</import>
6 </macros> 6 </macros>
7 7
8 <requirements> 8 <expand macro="requirements" />
9 <expand macro="requirement_package_numpy" />
10 <expand macro="requirement_package_rseqc" />
11 </requirements>
12 9
13 <expand macro="stdio" /> 10 <expand macro="stdio" />
14 11
15 <version_command><![CDATA[read_distribution.py --version]]></version_command> 12 <version_command><![CDATA[read_distribution.py --version]]></version_command>
16 13
17 <command><![CDATA[ 14 <command><![CDATA[
18 read_distribution.py -i $input -r $refgene > $output 15 read_distribution.py -i '${input}' -r '${refgene}' > '${output}'
19 ]]> 16 ]]>
20 </command> 17 </command>
21 18
22 <inputs> 19 <inputs>
23 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/> 20 <expand macro="bam_sam_param" />
24 <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/> 21 <expand macro="refgene_param" />
25 </inputs> 22 </inputs>
26 23
27 <outputs> 24 <outputs>
28 <data format="txt" name="output" /> 25 <data format="txt" name="output" />
29 </outputs> 26 </outputs>
87 TES_down_1kb 18298543 266161 14.55 84 TES_down_1kb 18298543 266161 14.55
88 TES_down_5kb 78900674 729997 9.25 85 TES_down_5kb 78900674 729997 9.25
89 TES_down_10kb 140361190 896882 6.39 86 TES_down_10kb 140361190 896882 6.39
90 =============== ============ =========== =========== 87 =============== ============ =========== ===========
91 88
92 ----- 89 @ABOUT@
93 90
94 About RSeQC
95 +++++++++++
96
97 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.
98
99 The RSeQC package is licensed under the GNU GPL v3 license.
100
101 .. image:: http://rseqc.sourceforge.net/_static/logo.png
102
103 .. _RSeQC: http://rseqc.sourceforge.net/
104 ]]> 91 ]]>
105 </help> 92 </help>
106 93
107 <expand macro="citations" /> 94 <expand macro="citations" />
108 95