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comparison infer_experiment.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
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50:f242ee103277 51:09846d5169fa
1 <tool id="rseqc_infer_experiment" name="Infer Experiment" version="2.4galaxy1"> 1 <tool id="rseqc_infer_experiment" name="Infer Experiment" version="@WRAPPER_VERSION@">
2 <description>speculates how RNA-seq were configured</description> 2 <description>speculates how RNA-seq were configured</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[infer_experiment.py --version]]></version_command> 12 <version_command><![CDATA[infer_experiment.py --version]]></version_command>
16 13
17 <command><![CDATA[ 14 <command><![CDATA[
18 infer_experiment.py -i $input -r $refgene 15 infer_experiment.py -i '${input}' -r '${refgene}'
19 --sample-size $sample_size 16 --sample-size ${sample_size}
20 --mapq $mapq 17 --mapq ${mapq}
21 > $output 18 > '${output}'
22 ]]> 19 ]]>
23 </command> 20 </command>
24 21
25 <inputs> 22 <inputs>
26 <param name="input" type="data" format="bam,sam" label="Input BAM/SAM file" help="(--input-file)"/> 23 <expand macro="bam_param" />
27 <param name="refgene" type="data" format="bed" label="Reference gene model in bed format" help="(--refgene)" /> 24 <expand macro="refgene_param" />
28 <param name="sample_size" type="integer" label="Number of reads sampled from SAM/BAM file (default = 200000)" value="200000" help="(--sample-size)"/> 25 <expand macro="sample_size_param" />
29 <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" /> 26 <expand macro="mapq_param" />
30 </inputs> 27 </inputs>
31 28
32 <outputs> 29 <outputs>
33 <data format="txt" name="output" /> 30 <data format="txt" name="output" />
34 </outputs> 31 </outputs>
132 Fraction of reads explained by other combinations: 0.0000 129 Fraction of reads explained by other combinations: 0.0000
133 ========================================================= 130 =========================================================
134 131
135 *Conclusion*: This is single-end, strand specific RNA-seq data. Strandness of reads are concordant with strandness of reference gene. 132 *Conclusion*: This is single-end, strand specific RNA-seq data. Strandness of reads are concordant with strandness of reference gene.
136 133
137 134 @ABOUT@
138 -----
139
140 About RSeQC
141 +++++++++++
142
143 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.
144
145 The RSeQC package is licensed under the GNU GPL v3 license.
146
147 .. image:: http://rseqc.sourceforge.net/_static/logo.png
148
149 .. _RSeQC: http://rseqc.sourceforge.net/
150 135
151 ]]> 136 ]]>
152 </help> 137 </help>
153 138
154 <expand macro="citations" /> 139 <expand macro="citations" />