Mercurial > repos > iuc > seqtk

comparison seqtk_mergepe.xml @ 16:48a51c72f5e7 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 05:58:58 -0400
parents 16f2535c08bf
children 069c8f0695ee
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15:16f2535c08bf 16:48a51c72f5e7
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 seqtk mergepe 10 seqtk mergepe
11 '$in_fq1' 11 '$in_fq1'
12 '$in_fq2' 12 '$in_fq2'
13 > '$default' 13 #echo "| gzip --no-name" if $in_fq1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
14 ]]></command> 14 ]]></command>
15 <inputs> 15 <inputs>
16 <param name="in_fq1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/> 16 <param name="in_fq1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
17 <param name="in_fq2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/> 17 <param name="in_fq2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
18 </inputs> 18 </inputs>
19 <outputs> 19 <outputs>
20 <data name="default" format_source="in_fq1" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/> 20 <data name="default" format_source="in_fq1" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/>
21 </outputs> 21 </outputs>
22 <tests> 22 <tests>
23 <test> 23 <test>
24 <param name="in_fq1" value="paired_dat1.fq"/> 24 <param name="in_fq1" value="paired_dat1.fq" ftype="fastqsanger"/>
25 <param name="in_fq2" value="paired_dat2.fq"/> 25 <param name="in_fq2" value="paired_dat2.fq" ftype="fastqsanger"/>
26 <output name="default" file="paired_dat.fq" ftype="fastq"/> 26 <output name="default" file="paired_dat.fq" ftype="fastqsanger"/>
27 </test>
28 <test>
29 <param name="in_fq1" value="paired_dat1.fq.gz" ftype="fastqsanger.gz"/>
30 <param name="in_fq2" value="paired_dat2.fq.gz" ftype="fastqsanger.gz"/>
31 <output name="default" file="paired_dat.fq.gz" ftype="fastqsanger.gz"/>
27 </test> 32 </test>
28 </tests> 33 </tests>
29 <help><![CDATA[ 34 <help><![CDATA[
30 **What it does** 35 **What it does**
31 36