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annotate bamToFastq.xml @ 48:2f457890d8c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
author iuc
date Tue, 11 Dec 2018 13:59:34 -0500
parents cb98f29aa1dc
children df28283b3778
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48
2f457890d8c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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1 <tool id="bedtools_bamtofastq" name="bedtools Convert from BAM to FastQ" version="@WRAPPER_VERSION@">
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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 $tags
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11 -i '$input'
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12 -fq '$output'
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13 #if $fq2:
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14 -fq2 '$output2'
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15 #end if
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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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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."/>
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20 <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="False" label="FASTQ for second end.
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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."/>
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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="${input.name} (as FASTQ)"/>
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25 <data format="fastq" name="output2" metadata_source="input" label="${input.name} (as FASTQ)">
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26 <filter>fq2 is True</filter>
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27 </data>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input" value="srma_in3.bam" ftype="bam" />
2f457890d8c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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32 <output name="output" file="bamToFastq_result1.fastq" ftype="fastq" />
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33 </test>
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34 </tests>
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35 <help>
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37 **What it does**
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39 bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.
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41 @REFERENCES@
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43 </help>
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44 <expand macro="citations" />
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45 </tool>