Mercurial > repos > iuc > seqtk
comparison seqtk_subseq.xml @ 4:ecf1c30da3a2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
author | iuc |
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date | Wed, 17 Oct 2018 05:59:21 -0400 |
parents | bc7d99f46a5d |
children | a09586d5149a |
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3:bc7d99f46a5d | 4:ecf1c30da3a2 |
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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. |