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annotate bam2wig.xml @ 33:073c77ce5e94

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export PYTHONPATH during install, note python 2.7 requirement
author lparsons
date Tue, 15 Oct 2013 12:58:55 -0400
parents 580ee0c4bc4e
children 8fbd165f8835
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32
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1 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="1.1">
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2 <description>
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3 converts all types of RNA-seq data from .bam to .wig
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="3.0.1">R</requirement>
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7 <requirement type="package" version="1.7.1">numpy</requirement>
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8 <requirement type="package" version="2.3.7">rseqc</requirement>
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9 </requirements>
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10 <command>
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11
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12 #import tempfile, os
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13 #set $tmp_input = tempfile.NamedTemporaryFile()
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14 #set $tmp_input_name = $input_singles_tmp_handle.name
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15 #silent $tmp_input.close()
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16
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17 ln -s "${input}" $tmp_input_name &amp;&amp;
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18 ln -s "${input.metadata.bam_index}" $tmp_input_name + ".bai" &amp;&amp;
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19 bam2wig.py -i "local_input.bam" -s $chromsize -o outfile
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21 #if str($strand_type.strand_specific) == "pair"
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22 -d
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23 #if str($strand_type.pair_type) == "sd"
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24 '1++,1--,2+-,2-+'
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25 #else
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26 '1+-,1-+,2++,2--'
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27 #end if
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28 #end if
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30 #if str($strand_type.strand_specific) == "single"
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31 -d
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32 #if str($strand_type.single_type) == "s"
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33 '++,--'
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34 #else
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35 '+-,-+'
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36 #end if
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37 #end if
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39 #if $wigsum.wigsum_type
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40 -t $wigsum.totalwig
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41 #end if
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43 #if $skipmultihits
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44 -u
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45 #end if
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46 ;
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47 rm $tmp_input_name + ".bai" ;
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48 rm $tmp_input_name
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49 </command>
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50 <inputs>
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51 <param name="input" type="data" label="Input .bam File" format="bam" />
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52 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" />
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53 <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" />
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54 <conditional name="wigsum">
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55 <param name="wigsum_type" type="boolean" label="Specify wigsum?" value="false">
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56 </param>
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57 <when value="true">
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58 <param name="totalwig" value="0" type="integer" label="specified wigsum" />
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59 </when>
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60 <when value="false"/>
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61 </conditional>
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62 <conditional name="strand_type">
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63 <param name="strand_specific" type="select" label="Strand-specific?" value="none">
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64 <option value="none">none</option>
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65 <option value="pair">Pair-End RNA-seq</option>
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66 <option value="single">Single-End RNA-seq</option>
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67 </param>
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68 <when value="pair">
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69 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd">
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70 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
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71 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
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72 </param>
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73 </when>
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74 <when value="single">
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75 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s">
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76 <option value="s">positive --> positive; negative --> negative</option>
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77 <option value="d">positive --> negative; negative --> positive</option>
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78 </param>
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79 </when>
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80 <when value="none"></when>
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81 </conditional>
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82 </inputs>
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83 <outputs>
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84 <data format="wig" name="output" from_work_dir="outfile.wig">
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85 <filter>strand_type['strand_specific'] == 'none'</filter>
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86 </data>
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87 <data format="wig" name="outputfwd" from_work_dir="outfile_Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)">
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88 <filter>strand_type['strand_specific'] != 'none'</filter>
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89 </data>
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90 <data format="wig" name="outputrv" from_work_dir="outfile_Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)">
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91 <filter>strand_type['strand_specific'] != 'none'</filter>
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92 </data>
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93 </outputs>
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94 <stdio>
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95 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
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96 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
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97 </stdio>
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98 <help>
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99 bam2wig.py
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100 ++++++++++
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101
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102 Visualization is the most straightforward and effective way to QC your RNA-seq
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103 data. For example, change of expression or new splicing can be easily checked
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104 by visually comparing two RNA-seq tracks using genome browser such as UCSC_,
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105 IGB_ and IGV_. `bam2wig.py` converts all types of RNA-seq data from BAM_
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106 format into wiggle_ format in one-stop. wiggle_ files can then be easily
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107 converted into bigwig_. Bigwig is indexed, binary format of wiggle file, and
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108 it's particular useful to display large, continuous dataset on genome
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109 browser.
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110
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111 Inputs
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112 ++++++++++++++
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113
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114 Input BAM file
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115 Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools.
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116
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117 Chromosome size file
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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.
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119
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120 Specified wigsum (default=none)
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121 Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization.
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122
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123 Skip multiple Hit reads
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124 skips multiple hit reads or only use uniquely mapped reads
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125
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126 Strand-specific (default=none)
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127 How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py
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128
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129 Outputs
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130 ++++++++++++++
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131
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132 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
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133 is strand specific, two wig files corresponding to Forward and Reverse will be generated.
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134
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135 -----
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136
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137 About RSeQC
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138 +++++++++++
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139
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140
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141 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.
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142
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143 The RSeQC package is licensed under the GNU GPL v3 license.
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144
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145 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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146
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147 .. _RSeQC: http://rseqc.sourceforge.net/
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148 .. _UCSC: http://genome.ucsc.edu/index.html
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149 .. _IGB: http://bioviz.org/igb/
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150 .. _IGV: http://www.broadinstitute.org/igv/home
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151 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
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152 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
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153 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
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154
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155 </help>
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156 </tool>