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annotate bamToFastq.xml @ 26:c0fbce5dc84a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:20 -0400
parents 5efc48568d8d
children cb98f29aa1dc
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5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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1 <tool id="bedtools_bamtofastq" name="Convert from BAM to FastQ" version="@WRAPPER_VERSION@.0">
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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5 </macros>
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6 <expand macro="requirements" />
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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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 $tags
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11 -i '$input'
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12 -fq '$output'
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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13 #if $fq2:
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14 -fq2 '$output2'
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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15 #end if
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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16 </command>
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17 <inputs>
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18 <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/>
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c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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19 <param name="tags" type="boolean" truevalue="-tags" falsevalue="" checked="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
c0fbce5dc84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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20 <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="False" label="FASTQ for second end.
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5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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21 Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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22 </inputs>
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23 <outputs>
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24 <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/>
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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25 <data format="fastq2" name="output2" metadata_source="input" label="${input.name} (as FASTQ)">
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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26 <filter>fq2 is True</filter>
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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27 </data>
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28 </outputs>
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29 <help>
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31 **What it does**
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5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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33 bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.
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35 @REFERENCES@
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37 </help>
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38 <expand macro="citations" />
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39 </tool>