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1 <tool id="tophatstatsPE" name="Tophat Stats PE" version="1.0">
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2 <description>Calculate mapping statistics from Tophat BAM files.</description>
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3 <command interpreter="perl">tophatstatsPE.pl $hits $fastq > $output</command>
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4 <inputs>
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5 <param name="hits" type="data" format="bam" label="BAM file produced by Tophat"/>
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6 <param name="fastq" type="data" format="fastq" label="Fastq file used to produce the BAM file" />
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7 </inputs>
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8 <outputs>
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9 <data format="txt" name="output" />
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10 </outputs>
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11 <tests>
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12 </tests>
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13 <help>
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14 **Tophat Stats PE**
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15
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16 This tool generates mapping statics from BAM files produced by
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17 Tophat. For paired-end experiments only one of the read files (R1
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18 or R2) needs to be provided.
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19
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20 **Example output:**
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21
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22 ::
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23
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24 Input files: /galaxy/database/files/001/dataset_1682.dat /galaxy/database/files/001/dataset_1680.dat
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25 73538 total read pairs in fastq file
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26 14429 (19.62%) read pairs with only one read in the pair mapped (14262 with unique alignments)
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27 36461 (49.58%) read pairs mapped with correct orientation and insert size (36366 with unique alignments)
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28 12169 (16.55%) read pairs mapped with correct orientation but wrong insert size (12063 with unique alignments)
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29 0.458333333333333 (0.00%) read pairs mapped with wrong orientation but correct insert size (0 with unique alignments)
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30 10478.5416666667 (14.25%) read pairs with no mapping
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31
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32
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33 **Credit**
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34
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35 John Garbe, University of Minnesota
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36
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37 </help>
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38 </tool>
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