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comparison seqtk_subseq.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
comparison
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15:16f2535c08bf 16:48a51c72f5e7
17 '$name_list' 17 '$name_list'
18 #end if 18 #end if
19 #if $t == '-t': 19 #if $t == '-t':
20 | awk 'BEGIN{print "chr\tunknown\tseq"}1' 20 | awk 'BEGIN{print "chr\tunknown\tseq"}1'
21 #end if 21 #end if
22 > '$default' 22 @CONDITIONAL_GZIP_OUT@
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <expand macro="in_faq"/> 25 <expand macro="in_faq"/>
26 <conditional name="source"> 26 <conditional name="source">
27 <param name="type" type="select" label="Select source of sequence choices"> 27 <param name="type" type="select" label="Select source of sequence choices">
51 <param name="type" value="name"/> 51 <param name="type" value="name"/>
52 <param name="t" value="False" /> 52 <param name="t" value="False" />
53 <param name="name_list" value="seqtk_subseq_list.txt"/> 53 <param name="name_list" value="seqtk_subseq_list.txt"/>
54 <output name="default" file="seqtk_subseq.out" ftype="fasta"/> 54 <output name="default" file="seqtk_subseq.out" ftype="fasta"/>
55 </test> 55 </test>
56 <test>
57 <param name="in_file" value="seqtk_subseq.fa.gz" ftype="fasta.gz"/>
58 <param name="type" value="name"/>
59 <param name="t" value="False" />
60 <param name="name_list" value="seqtk_subseq_list.txt"/>
61 <output name="default" file="seqtk_subseq.out.gz" ftype="fasta.gz"/>
62 </test>
56 </tests> 63 </tests>
57 <help><![CDATA[ 64 <help><![CDATA[
58 **What it does** 65 **What it does**
59 66
60 Given a list of newline separated IDs from a fasta file, this will extract those named fasta sequences from the input file. 67 Given a list of newline separated IDs from a fasta file, this will extract those named fasta sequences from the input file.