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1 <tool id="bedtools_bamtofastq" name="Convert from BAM to FastQ" version="@WRAPPER_VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 bedtools bamtofastq
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10 $tags
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11 $fq2
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12 -i '$input'
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13 -fq '$output'
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14 </command>
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15 <inputs>
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16 <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/>
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17 <param name="tags" type="boolean" truevalue="-tags" falsevalue="" selected="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
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18 <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" selected="False" label="ASTQ for second end. Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
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19 </inputs>
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20 <outputs>
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21 <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/>
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22 </outputs>
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23 <help>
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24
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25 **What it does**
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26
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27 bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.
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28
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29 @REFERENCES@
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30
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31 </help>
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32 </tool>
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