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annotate bamToFastq.xml @ 50:df28283b3778 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:54:22 -0400
parents 2f457890d8c8
children
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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1 <tool id="bedtools_bamtofastq" name="bedtools Convert from BAM to FastQ" version="@TOOL_VERSION@">
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2 <description></description>
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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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>
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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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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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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8 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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9 bedtools bamtofastq
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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10 $tags
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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11 -i '$input'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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12 -fq '$output'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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13 #if $fq2:
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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14 -fq2 '$output2'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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15 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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16 ]]></command>
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17 <inputs>
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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18 <param name="input" type="data" format="bam" label="Convert the following BAM file to FASTQ"/>
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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19 <param argument="-tags" type="boolean" truevalue="-tags" falsevalue="" checked="false" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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20 <param argument="-fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="false" label="FASTQ for second end"
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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21 help="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>
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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23 <outputs>
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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24 <data name="output" format="fastq" metadata_source="input" label="${input.name} (as FASTQ)"/>
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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25 <data name="output2" format="fastq" metadata_source="input" label="${input.name} (as FASTQ)">
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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>
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
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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" />
2f457890d8c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 **What it does**
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38 bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.
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40 @REFERENCES@
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41 ]]></help>
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42 <expand macro="citations" />
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43 </tool>