Mercurial > repos > iuc > seqtk

comparison seqtk_trimfq.xml @ 4:ecf1c30da3a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
author iuc
date Wed, 17 Oct 2018 05:59:21 -0400
parents bc7d99f46a5d
children a09586d5149a
comparison
equal deleted inserted replaced
3:bc7d99f46a5d 4:ecf1c30da3a2
14 #else: 14 #else:
15 -b $mode.b 15 -b $mode.b
16 -e $mode.e 16 -e $mode.e
17 #end if 17 #end if
18 '$in_file' 18 '$in_file'
19 > '$default' 19 @CONDITIONAL_GZIP_OUT@
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 <expand macro="in_faq"/> 22 <expand macro="in_faq"/>
23 <conditional name="mode"> 23 <conditional name="mode">
24 <param name="mode_select" type="select" label="Mode for trimming FASTQ File"> 24 <param name="mode_select" type="select" label="Mode for trimming FASTQ File">
38 <outputs> 38 <outputs>
39 <data name="default" format_source="in_file" label="$in_file.name trimmed"/> 39 <data name="default" format_source="in_file" label="$in_file.name trimmed"/>
40 </outputs> 40 </outputs>
41 <tests> 41 <tests>
42 <test> 42 <test>
43 <param name="in_file" value="seqtk_trimfq.fq"/> 43 <param name="in_file" value="seqtk_trimfq.fq" ftype="fastqsanger"/>
44 <param name="mode_select" value="quality"/> 44 <param name="mode_select" value="quality"/>
45 <param name="q" value="0.05"/> 45 <param name="q" value="0.05"/>
46 <param name="l" value="30"/> 46 <param name="l" value="30"/>
47 <output name="default" file="seqtk_trimfq_default.fq" ftype="fastq"/> 47 <output name="default" file="seqtk_trimfq_default.fq" ftype="fastqsanger"/>
48 </test> 48 </test>
49 <test> 49 <test>
50 <param name="in_file" value="seqtk_trimfq.fq"/> 50 <param name="in_file" value="seqtk_trimfq.fq" ftype="fastqsanger"/>
51 <param name="mode_select" value="position"/> 51 <param name="mode_select" value="position"/>
52 <param name="b" value="5"/> 52 <param name="b" value="5"/>
53 <param name="e" value="5"/> 53 <param name="e" value="5"/>
54 <output name="default" file="seqtk_trimfq_be.fq" ftype="fastq"/> 54 <output name="default" file="seqtk_trimfq_be.fq" ftype="fastqsanger"/>
55 </test>
56 <test>
57 <param name="in_file" value="seqtk_trimfq.fq.gz" ftype="fastqsanger.gz"/>
58 <param name="mode_select" value="position"/>
59 <param name="b" value="5"/>
60 <param name="e" value="5"/>
61 <output name="default" file="seqtk_trimfq_be.fq.gz" ftype="fastqsanger.gz"/>
55 </test> 62 </test>
56 </tests> 63 </tests>
57 <help><![CDATA[ 64 <help><![CDATA[
58 **What it does** 65 **What it does**
59 66