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comparison seqtk_subseq.xml @ 0:e0a0fd938de4 draft

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author iuc
date Thu, 05 Feb 2015 11:52:40 -0500
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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>
83 </tool>