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comparison bamToFastq.xml @ 34:dde39ba9c031 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 05:55:48 -0400
parents 4f7a5ccd2ae9
children
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_bamtofastq" name="bedtools Convert from BAM to FastQ" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_bamtofastq" name="bedtools Convert from BAM to FastQ" version="@TOOL_VERSION@">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command><![CDATA[
9 bedtools bamtofastq 9 bedtools bamtofastq
10 $tags 10 $tags
11 -i '$input' 11 -i '$input'
12 -fq '$output' 12 -fq '$output'
13 #if $fq2: 13 #if $fq2:
14 -fq2 '$output2' 14 -fq2 '$output2'
15 #end if 15 #end if
16 </command> 16 ]]></command>
17 <inputs> 17 <inputs>
18 <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/> 18 <param name="input" type="data" format="bam" label="Convert the following BAM file to FASTQ"/>
19 <param name="tags" type="boolean" truevalue="-tags" falsevalue="" checked="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/> 19 <param argument="-tags" type="boolean" truevalue="-tags" falsevalue="" checked="false" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
20 <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="False" label="FASTQ for second end. 20 <param argument="-fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="false" label="FASTQ for second end"
21 Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/> 21 help="Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
22 </inputs> 22 </inputs>
23 <outputs> 23 <outputs>
24 <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/> 24 <data name="output" format="fastq" metadata_source="input" label="${input.name} (as FASTQ)"/>
25 <data format="fastq" name="output2" metadata_source="input" label="${input.name} (as FASTQ)"> 25 <data name="output2" format="fastq" metadata_source="input" label="${input.name} (as FASTQ)">
26 <filter>fq2 is True</filter> 26 <filter>fq2 is True</filter>
27 </data> 27 </data>
28 </outputs> 28 </outputs>
29 <tests> 29 <tests>
30 <test> 30 <test>
31 <param name="input" value="srma_in3.bam" ftype="bam" /> 31 <param name="input" value="srma_in3.bam" ftype="bam" />
32 <output name="output" file="bamToFastq_result1.fastq" ftype="fastq" /> 32 <output name="output" file="bamToFastq_result1.fastq" ftype="fastq" />
33 </test> 33 </test>
34 </tests> 34 </tests>
35 <help> 35 <help><![CDATA[
36
37 **What it does** 36 **What it does**
38 37
39 bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format. 38 bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.
40 39
41 @REFERENCES@ 40 @REFERENCES@
42 41 ]]></help>
43 </help>
44 <expand macro="citations" /> 42 <expand macro="citations" />
45 </tool> 43 </tool>