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comparison bam2wig.xml @ 32:580ee0c4bc4e

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Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
author lparsons
date Mon, 07 Oct 2013 15:01:13 -0400
parents cc5eaa9376d8
children 8fbd165f8835
comparison
equal deleted inserted replaced
31:cc5eaa9376d8 32:580ee0c4bc4e
1 <tool id="bam2wig" name="BAM to Wiggle" version="1.1"> 1 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="1.1">
2 <description> 2 <description>
3 converts all types of RNA-seq data from .bam to .wig 3 converts all types of RNA-seq data from .bam to .wig
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="2.11.0">R</requirement> 6 <requirement type="package" version="3.0.1">R</requirement>
7 <requirement type="package" version="1.7.1">numpy</requirement> 7 <requirement type="package" version="1.7.1">numpy</requirement>
8 <requirement type="package" version="2.3.7">rseqc</requirement> 8 <requirement type="package" version="2.3.7">rseqc</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command>
11 ln -s "${input}" "local_input.bam" &amp;&amp;
12 ln -s "${input.metadata.bam_index}" "local_input.bam.bai" &amp;&amp;
13 bam2wig.py -i "local_input.bam" -s $chromsize -o outfile
14 11
15 #if str($strand_type.strand_specific) == "pair" 12 #import tempfile, os
16 -d 13 #set $tmp_input = tempfile.NamedTemporaryFile()
17 #if str($strand_type.pair_type) == "sd" 14 #set $tmp_input_name = $input_singles_tmp_handle.name
18 '1++,1--,2+-,2-+' 15 #silent $tmp_input.close()
19 #else
20 '1+-,1-+,2++,2--'
21 #end if
22 #end if
23 16
24 #if str($strand_type.strand_specific) == "single" 17 ln -s "${input}" $tmp_input_name &amp;&amp;
25 -d 18 ln -s "${input.metadata.bam_index}" $tmp_input_name + ".bai" &amp;&amp;
26 #if str($strand_type.single_type) == "s" 19 bam2wig.py -i "local_input.bam" -s $chromsize -o outfile
27 '++,--'
28 #else
29 '+-,-+'
30 #end if
31 #end if
32 20
33 #if $wigsum.wigsum_type 21 #if str($strand_type.strand_specific) == "pair"
34 -t $wigsum.totalwig 22 -d
35 #end if 23 #if str($strand_type.pair_type) == "sd"
24 '1++,1--,2+-,2-+'
25 #else
26 '1+-,1-+,2++,2--'
27 #end if
28 #end if
36 29
37 #if $skipmultihits 30 #if str($strand_type.strand_specific) == "single"
38 -u 31 -d
39 #end if 32 #if str($strand_type.single_type) == "s"
40 </command> 33 '++,--'
41 <inputs> 34 #else
42 <param name="input" type="data" label="Input .bam File" format="bam" /> 35 '+-,-+'
43 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" /> 36 #end if
44 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" /> 37 #end if
45 <conditional name="wigsum"> 38
46 <param name="wigsum_type" type="boolean" label="Specify wigsum?" value="false"> 39 #if $wigsum.wigsum_type
47 </param> 40 -t $wigsum.totalwig
48 <when value="true"> 41 #end if
49 <param name="totalwig" value="0" type="integer" label="specified wigsum" /> 42
50 </when> 43 #if $skipmultihits
51 <when value="false"></when> 44 -u
52 </conditional> 45 #end if
53 <conditional name="strand_type"> 46 ;
54 <param name="strand_specific" type="select" label="Strand-specific?" value="none"> 47 rm $tmp_input_name + ".bai" ;
55 <option value="none">none</option> 48 rm $tmp_input_name
56 <option value="pair">Pair-End RNA-seq</option> 49 </command>
57 <option value="single">Single-End RNA-seq</option> 50 <inputs>
58 </param> 51 <param name="input" type="data" label="Input .bam File" format="bam" />
59 <when value="pair"> 52 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" />
60 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd"> 53 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" />
61 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option> 54 <conditional name="wigsum">
62 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option> 55 <param name="wigsum_type" type="boolean" label="Specify wigsum?" value="false">
63 </param> 56 </param>
64 </when> 57 <when value="true">
65 <when value="single"> 58 <param name="totalwig" value="0" type="integer" label="specified wigsum" />
66 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s"> 59 </when>
67 <option value="s">positive --> positive; negative --> negative</option> 60 <when value="false"/>
68 <option value="d">positive --> negative; negative --> positive</option> 61 </conditional>
69 </param> 62 <conditional name="strand_type">
70 </when> 63 <param name="strand_specific" type="select" label="Strand-specific?" value="none">
71 <when value="none"></when> 64 <option value="none">none</option>
72 </conditional> 65 <option value="pair">Pair-End RNA-seq</option>
73 </inputs> 66 <option value="single">Single-End RNA-seq</option>
74 <outputs> 67 </param>
75 <data format="wig" name="output" from_work_dir="outfile.wig"> 68 <when value="pair">
76 <filter>strand_type['strand_specific'] == 'none'</filter> 69 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd">
77 </data> 70 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
78 <data format="wig" name="outputfwd" from_work_dir="outfile_Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)"> 71 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
79 <filter>strand_type['strand_specific'] != 'none'</filter> 72 </param>
80 </data> 73 </when>
81 <data format="wig" name="outputrv" from_work_dir="outfile_Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)"> 74 <when value="single">
82 <filter>strand_type['strand_specific'] != 'none'</filter> 75 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s">
83 </data> 76 <option value="s">positive --> positive; negative --> negative</option>
84 </outputs> 77 <option value="d">positive --> negative; negative --> positive</option>
78 </param>
79 </when>
80 <when value="none"></when>
81 </conditional>
82 </inputs>
83 <outputs>
84 <data format="wig" name="output" from_work_dir="outfile.wig">
85 <filter>strand_type['strand_specific'] == 'none'</filter>
86 </data>
87 <data format="wig" name="outputfwd" from_work_dir="outfile_Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)">
88 <filter>strand_type['strand_specific'] != 'none'</filter>
89 </data>
90 <data format="wig" name="outputrv" from_work_dir="outfile_Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)">
91 <filter>strand_type['strand_specific'] != 'none'</filter>
92 </data>
93 </outputs>
85 <stdio> 94 <stdio>
86 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 95 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
87 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 96 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
88 </stdio> 97 </stdio>
89 <help> 98 <help>
90 bam2wig.py 99 bam2wig.py
91 ++++++++++ 100 ++++++++++
92 101
93 Visualization is the most straightforward and effective way to QC your RNA-seq 102 Visualization is the most straightforward and effective way to QC your RNA-seq
94 data. For example, change of expression or new splicing can be easily checked 103 data. For example, change of expression or new splicing can be easily checked
101 110
102 Inputs 111 Inputs
103 ++++++++++++++ 112 ++++++++++++++
104 113
105 Input BAM file 114 Input BAM file
106 Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools. 115 Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools.
107 116
108 Chromosome size file 117 Chromosome size file
109 Tab or space separated text file with 2 columns: first column is chromosome name, second column is size of the chromosome. Chromosome names (such as "chr1") should be consistent between this file and BAM file. 118 Tab or space separated text file with 2 columns: first column is chromosome name, second column is size of the chromosome. Chromosome names (such as "chr1") should be consistent between this file and BAM file.
110 119
111 Specified wigsum (default=none) 120 Specified wigsum (default=none)
112 Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization. 121 Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization.
113 122
114 Skip multiple Hit reads 123 Skip multiple Hit reads
115 skips multiple hit reads or only use uniquely mapped reads 124 skips multiple hit reads or only use uniquely mapped reads
116 125
117 Strand-specific (default=none) 126 Strand-specific (default=none)
118 How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py 127 How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py
119 128
120 Outputs 129 Outputs
121 ++++++++++++++ 130 ++++++++++++++
122 131
123 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
141 .. _IGV: http://www.broadinstitute.org/igv/home 150 .. _IGV: http://www.broadinstitute.org/igv/home
142 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html 151 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
143 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html 152 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
144 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1 153 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
145 154
146 </help> 155 </help>
147 </tool> 156 </tool>