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comparison bam2wig.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 080fd5739bb4
comparison
equal deleted inserted replaced
50:f242ee103277 51:09846d5169fa
1 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="2.4galaxy1"> 1 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@WRAPPER_VERSION@">
2 <description> 2 <description>
3 converts all types of RNA-seq data from .bam to .wig 3 converts all types of RNA-seq data from .bam to .wig
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_r" />
12 <expand macro="requirement_package_numpy" />
13 <expand macro="requirement_package_rseqc" />
14 </requirements>
15 11
16 <expand macro="stdio" /> 12 <expand macro="stdio" />
17 13
18 <version_command><![CDATA[bam2wig.py --version]]></version_command> 14 <version_command><![CDATA[bam2wig.py --version]]></version_command>
19 15
20 <command><![CDATA[ 16 <command><![CDATA[
21 ln -sfn '${input}' 'input.bam' && 17 ln -sf '${input}' 'input.bam' &&
22 ln -sfn '${input.metadata.bam_index}' 'input.bam.bai' && 18 ln -sf '${input.metadata.bam_index}' 'input.bam.bai' &&
23 bam2wig.py -i input.bam -s $chromsize -o outfile 19 bam2wig.py -i 'input.bam' -s '${chromsize}' -o outfile
24 20
25 #if str($strand_type.strand_specific) == "pair" 21 #if str($strand_type.strand_specific) == "pair"
26 -d 22 -d
27 #if str($strand_type.pair_type) == "sd" 23 #if str($strand_type.pair_type) == "sd"
28 '1++,1--,2+-,2-+' 24 '1++,1--,2+-,2-+'
38 #else 34 #else
39 '+-,-+' 35 '+-,-+'
40 #end if 36 #end if
41 #end if 37 #end if
42 38
43 #if $wigsum.wigsum_type 39 #if str($wigsum_type.wigsum_type_selector) == "normalize":
44 -t $wigsum.totalwig 40 -t ${wigsum.totalwig}
45 #end if 41 #end if
46 #if $multihits.skipmultihits 42
47 --skip-multi-hits 43 @MULTIHITS@
48 --mapq=$multihits.mapq
49 #end if
50 2>&1
51 ]]> 44 ]]>
52 </command> 45 </command>
53 <inputs> 46 <inputs>
54 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/> 47 <expand macro="bam_param" />
55 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/> 48 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/>
56 49 <expand macro="multihits_param" />
57 <conditional name="multihits"> 50 <conditional name="wigsum_type">
58 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" help="(--skip-multi-hits)" /> 51 <param name="wigsum_type_selector" type="select" label="Normalization">
59 <when value="true"> 52 <option value="normalize">Normalize to specified sum</option>
60 <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" /> 53 <option value="raw" selected="true">Do not normalize</option>
54 </param>
55 <when value="normalize">
56 <param name="totalwig" value="" type="integer" label="specified wigsum" help="(--wigsum)"/>
61 </when> 57 </when>
62 <when value="false" /> 58 <when value="raw"/>
63 </conditional> 59 </conditional>
64 60 <expand macro="strand_type_param" />
65 <conditional name="wigsum">
66 <param name="wigsum_type" type="boolean" label="Specify wigsum?" value="false">
67 </param>
68 <when value="true">
69 <param name="totalwig" value="0" type="integer" label="specified wigsum" help="(--wigsum)"/>
70 </when>
71 <when value="false"/>
72 </conditional>
73
74 <conditional name="strand_type">
75 <param name="strand_specific" type="select" label="Strand-specific?" value="none">
76 <option value="none">none</option>
77 <option value="pair">Pair-End RNA-seq</option>
78 <option value="single">Single-End RNA-seq</option>
79 </param>
80 <when value="pair">
81 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd" help="(--strand)">
82 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
83 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
84 </param>
85 </when>
86 <when value="single">
87 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s" help="(--strand)">
88 <option value="s">positive --> positive; negative --> negative</option>
89 <option value="d">positive --> negative; negative --> positive</option>
90 </param>
91 </when>
92 <when value="none"></when>
93 </conditional>
94 </inputs> 61 </inputs>
95 62
96 <outputs> 63 <outputs>
97 <data format="wig" name="output" from_work_dir="outfile.wig"> 64 <data format="wig" name="output" from_work_dir="outfile.wig">
98 <filter>strand_type['strand_specific'] == 'none'</filter> 65 <filter>strand_type['strand_specific'] == 'none'</filter>
112 <output name="output" file="testwig.wig"/> 79 <output name="output" file="testwig.wig"/>
113 </test> 80 </test>
114 <test> 81 <test>
115 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 82 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
116 <param name="chromsize" value="hg19.chrom.sizes"/> 83 <param name="chromsize" value="hg19.chrom.sizes"/>
117 <param name="skipmultihits" value="True"/> 84 <param name="multihits_type.multihits_type_selector" value="skipmultihits"/>
118 <param name="mapq" value="20"/> 85 <param name="multihits_type.mapq" value="20"/>
119 <output name="output" file="testwig.wig"/> 86 <output name="output" file="testwig.wig"/>
120 </test> 87 </test>
121 <test> 88 <test>
122 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 89 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
123 <param name="chromsize" value="hg19.chrom.sizes"/> 90 <param name="chromsize" value="hg19.chrom.sizes"/>
163 ++++++++++++++ 130 ++++++++++++++
164 131
165 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq 132 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
166 is strand specific, two wig files corresponding to Forward and Reverse will be generated. 133 is strand specific, two wig files corresponding to Forward and Reverse will be generated.
167 134
168 ----- 135 @ABOUT@
169
170 About RSeQC
171 +++++++++++
172
173 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.
174
175 The RSeQC package is licensed under the GNU GPL v3 license.
176
177 .. image:: http://rseqc.sourceforge.net/_static/logo.png
178
179 .. _RSeQC: http://rseqc.sourceforge.net/
180 136
181 .. _UCSC: http://genome.ucsc.edu/index.html 137 .. _UCSC: http://genome.ucsc.edu/index.html
182 .. _IGB: http://bioviz.org/igb/ 138 .. _IGB: http://bioviz.org/igb/
183 .. _IGV: http://www.broadinstitute.org/igv/home 139 .. _IGV: http://software.broadinstitute.org/software/igv/
184 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html 140 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
185 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html 141 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
186 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1 142 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
187 ]]> 143 ]]>
188 </help> 144 </help>