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1 <tool id="RPKM_count" name="RPKM Count">
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2 <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.18">samtools</requirement>
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5 <requirement type="package" version="2.3.7">rseqc</requirement>
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6 </requirements>
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7 <command interpreter="python"> samtoolshelper.py RPKM_count.py -i $input -o output -r $refgene
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8
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9 #if $nx
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10 -x
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11 #end if
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12
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13 #if str($strand_type.strand_specific) == "pair"
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14 -d
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15 #if str($strand_type.pair_type) == "sd"
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16 '1++,1--,2+-,2-+'
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17 #else
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18 '1+-,1-+,2++,2--'
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19 #end if
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20 #end if
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21
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22 #if str($strand_type.strand_specific) == "single"
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23 -d
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24 #if str($strand_type.single_type) == "s"
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25 '++,--'
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26 #else
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27 '+-,-+'
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28 #end if
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29 #end if
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30
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31 #if $skiphits
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32 -u
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33 #end if
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34
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35 #if $onlyexonic
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36 -e
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37 #end if
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38
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39 </command>
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40 <inputs>
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41 <param name="input" type="data" format="bam" label="input bam/sam file" />
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42 <param name="refgene" type="data" format="bed" label="Reference gene model" />
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43 <conditional name="strand_type">
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44 <param name="strand_specific" type="select" label="Strand-specific?" value="None">
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45 <option value="none">None</option>
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46 <option value="pair">Pair-End RNA-seq</option>
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47 <option value="single">Single-End RNA-seq</option>
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48 </param>
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49 <when value="pair">
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50 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd">
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51 <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
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52 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
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53 </param>
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54 </when>
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55 <when value="single">
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56 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s">
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57 <option value="s">positive --> positive; negative --> negative</option>
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58 <option value="d">positive --> negative; negative --> positive</option>
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59 </param>
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60 </when>
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61 <when value="none"></when>
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62 </conditional>
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63 <param name="skiphits" type="boolean" value="false" label="Skip Multiple Hit Reads" />
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64 <param name="onlyexonic" type="boolean" value="false" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" />
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65 </inputs>
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66 <outputs>
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67 <data format="xls" name="outputxls" from_work_dir="output_read_count.xls"/>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="input" value="Pairend_nonStrandSpecific_36mer_Human_hg19.bam" />
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72 <param name="refgene" value="hg19_RefSeq.bed" />
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73 <output name="outputxls" file="rpkmctout_read_count.xls" />
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74 </test>
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75 </tests>
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76 <help>
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77 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
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78
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79 -----
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80
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81 About RSeQC
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82 +++++++++++
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83
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84 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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85
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86 The RSeQC package is licensed under the GNU GPL v3 license.
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87
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88 Inputs
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89 ++++++++++++++
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90
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91 Input BAM/SAM file
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92 Alignment file in BAM/SAM format.
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93
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94 Reference gene model
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95 Gene model in BED format.
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96
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97 Strand sequencing type (default=none)
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98 See Infer Experiment tool if uncertain.
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99
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100 Options
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101 ++++++++++++++
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102
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103 Skip Multiple Hit Reads
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104 Use Multiple hit reads or use only uniquely mapped reads.
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105
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106 Only use exonic reads
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107 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads.
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108
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109 </help>
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110 </tool>
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