Mercurial > repos > iuc > seqtk
annotate seqtk_subseq.xml @ 8:d3b46dec1f5e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit e5a5ad091c621348dc6ce2df861475ebc54a380e
| author | iuc |
|---|---|
| date | Tue, 13 Oct 2015 17:27:35 -0400 |
| parents | 55e75a28fde7 |
| children | 16f2535c08bf |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool id="seqtk_subseq" name="seqtk_subseq" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>extract subsequences from FASTA/Q files</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="stdio"/> | |
| 9 <command><![CDATA[seqtk subseq $t | |
| 10 -l $l | |
| 11 $in_file | |
| 12 | |
| 13 #if $source.type == 'bed': | |
| 14 $in_bed | |
| 15 #else | |
| 16 $name_list | |
| 17 #end if | |
| 18 | |
| 19 #if $t == '-t': | |
| 20 | awk 'BEGIN{print "chr\tunknown\tseq"}1' | |
| 21 #end if | |
| 22 | |
| 23 > $default]]></command> | |
| 24 <inputs> | |
| 25 <param name="in_file" type="data" format="fasta,fastq" label="Input fasta/q file"/> | |
| 26 <conditional name="source"> | |
| 27 <param name="type" type="select" label="Select source of sequence choices"> | |
| 28 <option value="bed">BED</option> | |
| 29 <option value="name">FASTA/Q ID list</option> | |
| 30 </param> | |
| 31 <when value="bed"> | |
| 32 <param name="in_bed" type="data" format="bed" label="Input BED file"/> | |
| 33 </when> | |
| 34 <when value="name"> | |
| 35 <param name="name_list" type="data" format="txt" label="Input fasta file"/> | |
| 36 </when> | |
| 37 </conditional> | |
| 38 <param label="TAB delimited output" help="(-t)" name="t" type="boolean" falsevalue="" truevalue="-t"/> | |
| 39 <param label="sequence line length" help="(-l)" name="l" type="integer" value="0"/> | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 <data format_source="in_file" hidden="false" name="default" label="Selected sequences from $in_file.name"> | |
| 43 <change_format> | |
| 44 <when input="t" value="-t" format="tabular"/> | |
| 45 </change_format> | |
| 46 </data> | |
| 47 </outputs> | |
| 48 <tests> | |
| 49 <test> | |
| 50 <param name="in_file" value="seqtk_subseq.fa"/> | |
| 51 <param name="type" value="name"/> | |
| 52 <param name="t" value="False" /> | |
| 53 <param name="name_list" value="seqtk_subseq_list.txt"/> | |
| 54 <output name="default" file="seqtk_subseq.out" ftype="fasta"/> | |
| 55 </test> | |
| 56 </tests> | |
| 57 <help><![CDATA[ | |
| 58 **What it does** | |
| 59 | |
| 60 Given a list of newline separated IDs from a fasta file, this will extract those named fasta sequences from the input file. | |
| 61 | |
| 62 :: | |
| 63 | |
| 64 # Input ID list | |
| 65 seq1 | |
| 66 | |
| 67 # Input fasta | |
| 68 >seq1 | |
| 69 ACGTMRWSYK | |
| 70 >seq2 | |
| 71 RWSYKACGTM | |
| 72 | |
| 73 results in | |
| 74 | |
| 75 :: | |
| 76 | |
| 77 # Output result | |
| 78 >seq1 | |
| 79 ACGTMRWSYK | |
| 80 | |
| 81 @ATTRIBUTION@ | |
| 82 ]]></help> | |
|
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55e75a28fde7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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83 <expand macro="citation" /> |
| 0 | 84 </tool> |