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comparison geneBody_coverage.xml @ 50:f242ee103277 draft

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
author lparsons
date Tue, 03 May 2016 16:36:57 -0400
parents 6b33e31bda10
children 09846d5169fa
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49:6b33e31bda10 50:f242ee103277
1 <tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="2.4galaxy1"> 1 <tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="2.4galaxy2">
2 <description> 2 <description>
3 Read coverage over gene body. 3 Read coverage over gene body.
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 <requirements>
11 <expand macro="requirement_package_r" /> 11 <expand macro="requirement_package_r" />
12 <expand macro="requirement_package_numpy" /> 12 <expand macro="requirement_package_numpy" />
13 <expand macro="requirement_package_rseqc" /> 13 <expand macro="requirement_package_rseqc" />
14 </requirements> 14 </requirements>
15 15
16 <expand macro="stdio" /> 16 <expand macro="stdio" />
17 17
18 <version_command><![CDATA[geneBody_coverage.py --version]]></version_command> 18 <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
19 19
20 <command><![CDATA[ 20 <command><![CDATA[
21 #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $input.display_name) 21 #for $i, $input in enumerate($inputs):
22 #set $fname = "d1_" + str($safename) + ".bam" 22 #set $index = $i+1
23 ln -s '${input}' '${fname}' && 23 #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $input.display_name)
24 ln -s '${input.metadata.bam_index}' '${fname}.bai' && 24 #set $fname = 'd' + str($index) + '_' + str($safename) + ".bam"
25 echo '${fname}' > input_list.txt && 25 ln -s '$input' '${fname}' &&
26 #for $i, $additional_input in enumerate($additionalinputs): 26 ln -s '$input.metadata.bam_index' '${fname}.bai' &&
27 #set $index = $i+2 27 echo '${fname}' >> input_list.txt &&
28 #set $safename = ''.join(c in '_0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' and c or '_' for c in $additional_input.file.display_name) 28 #end for
29 #set $fname = 'd' + str($index) + '_' + str($safename) + ".bam" 29 geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output
30 ln -s '$additional_input.file' '${fname}' && 30 ]]>
31 ln -s '$additional_input.file.metadata.bam_index' '${fname}.bai' && 31 </command>
32 echo '${fname}' >> input_list.txt &&
33 #end for
34 geneBody_coverage.py -i input_list.txt -r $refgene --minimum_length $minimum_length -o output
35 ]]>
36 </command>
37 32
38 <inputs> 33 <inputs>
39 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/> 34 <param name="inputs" type="data" label="Input .bam File(s)" format="bam" help="(--input-file)" multiple="true"/>
40 <repeat name="additionalinputs" title="Additional input .bam files"> 35 <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
41 <param name="file" type="data" label="Additional input .bam file" format="bam" /> 36 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length in bp (default: 100)" help="mRNA that are shorter than this value will be skipped (--minimum_length)." />
42 </repeat> 37 </inputs>
43 <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
44 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length in bp (default: 100)" help="mRNA that are shorter than this value will be skipped (--minimum_length)." />
45 </inputs>
46 38
47 <outputs> 39 <outputs>
48 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves PDF)" /> 40 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves PDF)" />
49 <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap PDF)"> 41 <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap PDF)">
50 <filter>len(additionalinputs) >= 2</filter> 42 <filter>len(inputs) >= 3</filter>
51 </data> 43 </data>
52 <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage.r" label="${tool.name} on ${on_string} (R Script)" /> 44 <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage.r" label="${tool.name} on ${on_string} (R Script)" />
53 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" /> 45 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
54 </outputs> 46 </outputs>
55 47
56 <tests> 48 <!-- PDF Files contain R version, must avoid checking for diff -->
57 <test> 49 <tests>
58 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 50 <test>
59 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/> 51 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
60 <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf"/> 52 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
61 <output name="outputr" file="output.geneBodyCoverage.r"/> 53 <!-- <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf"/> -->
62 <output name="outputtxt" file="output.geneBodyCoverage.txt"/> 54 <output name="outputr" file="output.geneBodyCoverage.r"/>
63 </test> 55 <output name="outputtxt" file="output.geneBodyCoverage.txt"/>
64 <test> 56 </test>
65 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 57 <test>
66 <param name="file_0" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 58 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
67 <param name="file_1" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 59 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
68 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/> 60 <!-- <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf"/> -->
69 <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf"/> 61 <!-- <output name="outputheatmappdf" file="output2.geneBodyCoverage.heatMap.pdf"/> -->
70 <output name="outputcurvespdf" file="output2.geneBodyCoverage.heatMap.pdf"/> 62 <output name="outputr" file="output2.geneBodycoverage.r"/>
71 <output name="outputr" file="output2.geneBodycoverage.r"/> 63 <output name="outputtxt" file="output2.geneBodyCoverage.txt"/>
72 <output name="outputtxt" file="output2.geneBodyCoverage.txt"/> 64 </test>
73 </test>
74 65
75 </tests> 66 </tests>
76 67
77 <help><![CDATA[ 68 <help><![CDATA[
78 geneBody_coverage.py 69 ## geneBody_coverage.py
79 ++++++++++++++++++++
80 70
81 Read coverage over gene body. This module is used to check if read coverage is uniform and if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates plots illustrating the coverage profile along the gene body. 71 Read coverage over gene body. This module is used to check if read coverage is uniform and if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates plots illustrating the coverage profile along the gene body.
82 72
83 If 3 or more BAM files were provided. This program generates a lineGraph and a heatmap. If fewer than 3 BAM files were provided, only lineGraph is generated. See below for examples. 73 If 3 or more BAM files were provided. This program generates a lineGraph and a heatmap. If fewer than 3 BAM files were provided, only lineGraph is generated. See below for examples.
84 74
85 When heatmap is generated, samples are ranked by the "skewness" of the coverage: Sample with best (worst) coverage will be displayed at the top (bottom) of the heatmap. 75 When heatmap is generated, samples are ranked by the "skewness" of the coverage: Sample with best (worst) coverage will be displayed at the top (bottom) of the heatmap.
86 Coverage skewness was measured by `Pearson’s skewness coefficients <http://en.wikipedia.org/wiki/Skewness#Pearson.27s_skewness_coefficients>`_ 76 Coverage skewness was measured by `Pearson’s skewness coefficients <http://en.wikipedia.org/wiki/Skewness#Pearson.27s_skewness_coefficients>`_
87 77
88 .. image:: http://rseqc.sourceforge.net/_images/geneBody_workflow.png 78 .. image:: http://rseqc.sourceforge.net/_images/geneBody_workflow.png
89 :width: 800 px 79 :width: 800 px
90 :scale: 80 % 80 :scale: 80 %
91 81
92 82
93 Inputs 83 ## Inputs
94 ++++++++++++++
95 84
96 Input BAM/SAM file 85 Input BAM/SAM file
97 Alignment file in BAM/SAM format. 86 Alignment file in BAM/SAM format.
98 87
99 Reference gene model 88 Reference gene model
100 Gene Model in BED format. 89 Gene Model in BED format.
101 90
102 Minimum mRNA length 91 Minimum mRNA length
103 Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100). 92 Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100).
104 93
105 Outputs 94 ## Outputs
106 ++++++++++++++ 95
107 Text 96 Text
108 Table that includes the data used to generate the plots 97 Table that includes the data used to generate the plots
109 98
110 R Script 99 R Script
111 R script file that reads the data and generates the plot 100 R script file that reads the data and generates the plot
112 101
113 PDF 102 PDF
114 The final plot, in PDF format 103 The final plot, in PDF format
115 104
116 Example plots: 105 Example plots:
117 .. image:: http://rseqc.sourceforge.net/_images/Aug_26.geneBodyCoverage.curves.png 106 .. image:: http://rseqc.sourceforge.net/_images/Aug_26.geneBodyCoverage.curves.png
118 :height: 600 px 107 :height: 600 px
119 :width: 600 px 108 :width: 600 px
120 :scale: 80 % 109 :scale: 80 %
121 110
122 .. image:: http://rseqc.sourceforge.net/_images/Aug_26.geneBodyCoverage.heatMap.png 111 .. image:: http://rseqc.sourceforge.net/_images/Aug_26.geneBodyCoverage.heatMap.png
123 :height: 600 px 112 :height: 600 px
124 :width: 600 px 113 :width: 600 px
125 :scale: 80 % 114 :scale: 80 %
126 115
127 ----- 116 ## About RSeQC
128 117
129 About RSeQC 118 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.
130 +++++++++++
131 119
132 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. 120 The RSeQC package is licensed under the GNU GPL v3 license.
133 121
134 The RSeQC package is licensed under the GNU GPL v3 license. 122 .. image:: http://rseqc.sourceforge.net/_static/logo.png
135 123
136 .. image:: http://rseqc.sourceforge.net/_static/logo.png 124 .. _RSeQC: http://rseqc.sourceforge.net/
125 ]]>
126 </help>
137 127
138 .. _RSeQC: http://rseqc.sourceforge.net/ 128 <expand macro="citations" />
139 ]]>
140 </help>
141
142 <expand macro="citations" />
143 129
144 </tool> 130 </tool>