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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 <help>
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70 .. image:: https://code.google.com/p/rseqc/logo?cct=1336721062
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71
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72 -----
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73
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74 About RSeQC
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75 +++++++++++
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76
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77 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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78
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79 The RSeQC package is licensed under the GNU GPL v3 license.
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80
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81 Inputs
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82 ++++++++++++++
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83
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84 Input BAM/SAM file
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85 Alignment file in BAM/SAM format.
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86
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87 Reference gene model
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88 Gene model in BED format.
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89
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90 Strand sequencing type (default=none)
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91 See Infer Experiment tool if uncertain.
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92
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93 Options
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94 ++++++++++++++
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95
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96 Skip Multiple Hit Reads
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97 Use Multiple hit reads or use only uniquely mapped reads.
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98
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99 Only use exonic reads
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100 Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads.
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101
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102 Sample Output
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103 ++++++++++++++
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104
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105 ===== ===== === ========= ===== =========== ============= ============= ======== ========
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106 chrom start end accession score gene strand tag count (+) tag count (-) RPKM (+) RPKM (-)
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107 ===== ===== === ========= ===== =========== ============= ============= ======== ========
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108 chr1 29213722 29313959 NM_001166007_intron_1 0 + 431 4329 0.086 0.863
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109 chr1 29314417 29319841 NM_001166007_intron_2 0 + 31 1 0.114 0.004
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110 chr1 29320054 29323726 NM_001166007_intron_3 0 + 32 0 0.174 0
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111 chr1 29323831 29338376 NM_001166007_intron_4 0 + 33 2 0.045 0.003
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112 chr1 29338419 29342203 NM_001166007_intron_5 0 + 7 0 0.037 0
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113 chr1 29342279 29344735 NM_001166007_intron_6 0 + 35 4 0.285 0.033
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114 chr1 29344954 29356911 NM_001166007_intron_7 0 + 34 2 0.057 0.003
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115 chr1 29356999 29359604 NM_001166007_intron_8 0 + 19 1 0.146 0.008
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116 chr1 29359757 29362337 NM_001166007_intron_9 0 + 31 0 0.24 0
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117 chr1 29362435 29365765 NM_001166007_intron_10 0 + 11 1 0.066 0.006
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118 chr1 29365938 29379615 NM_001166007_intron_11 0 + 63 0 0.092 0
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119 chr1 29379824 29391493 NM_001166007_intron_12 0 + 383 8 0.656 0.014
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120 chr1 29391670 29424318 NM_001166007_intron_13 0 + 817 10 0.5 0.006
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121 chr1 29424447 29435847 NM_001166007_intron_14 0 + 28 0 0.049 0
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122 chr1 29435949 29438879 NM_001166007_intron_15 0 + 12 0 0.082 0
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123 chr1 29438960 29442210 NM_001166007_intron_16 0 + 22 2 0.135 0.012
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124 chr1 29442315 29443330 NM_001166007_intron_17 0 + 9 0 0.177 0
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125 chr1 29213602 29213722 NM_001166007_exon_1 0 + 164 0 27.321 0
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126 chr1 29313959 29314417 NM_001166007_exon_2 0 + 1699 4 74.158 0.175
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127 chr1 29319841 29320054 NM_001166007_exon_3 0 + 528 1 49.554 0.094
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128 chr1 29323726 29323831 NM_001166007_exon_4 0 + 168 0 31.985 0
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129 chr1 29338376 29338419 NM_001166007_exon_5 0 + 88 0 40.911 0
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130 chr1 29342203 29342279 NM_001166007_exon_6 0 + 114 3 29.986 0.789
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131 chr1 29344735 29344954 NM_001166007_exon_7 0 + 290 10 26.472 0.913
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132 chr1 29356911 29356999 NM_001166007_exon_8 0 + 146 1 33.166 0.227
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133 chr1 29359604 29359757 NM_001166007_exon_9 0 + 404 11 52.786 1.437
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134 chr1 29362337 29362435 NM_001166007_exon_10 0 + 85 7 17.339 1.428
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135 chr1 29365765 29365938 NM_001166007_exon_11 0 + 198 2 22.88 0.231
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136 chr1 29379615 29379824 NM_001166007_exon_12 0 + 306 5 29.269 0.478
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137 chr1 29391493 29391670 NM_001166007_exon_13 0 + 243 7 27.445 0.791
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138 chr1 29424318 29424447 NM_001166007_exon_14 0 + 298 7 46.18 1.085
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139 chr1 29435847 29435949 NM_001166007_exon_15 0 + 396 8 77.611 1.568
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140 chr1 29438879 29438960 NM_001166007_exon_16 0 + 307 0 75.767 0
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141 chr1 29442210 29442315 NM_001166007_exon_17 0 + 138 0 26.273 0
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142 chr1 29443330 29446558 NM_001166007_exon_18 0 + 2434 84 15.074 0.52
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143 chr1 29213602 29446558 NM_001166007_mRNA 0 + 8006 150 27.704 0.519
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144 ===== ===== === ========= ===== =========== ============= ============= ======== ========
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145
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146 </help>
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147 </tool>
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