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comparison seqtk_mergefa.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_mergefa" name="seqtk_mergefa" version="@WRAPPER_VERSION@.0">
3 <description>merge two 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 mergefa -q $q
10 $i
11 $m
12 $r
13 $h
14
15 $in_fa1
16 $in_fa2
17
18 > $default]]></command>
19 <inputs>
20 <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
21 <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
22 <param label="quality threshold" help="(-q)" name="q" type="integer" value="0"/>
23 <param checked="false" label="take intersection" help="(-i)" name="i" type="boolean" falsevalue="" truevalue="-i"/>
24 <param checked="false" label="convert to lowercase when one of the input base is N" help="(-m)" name="m" type="boolean" falsevalue="" truevalue="-m"/>
25 <param checked="false" label="pick a random allele from het" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/>
26 <param checked="false" label="suppress hets in the input" help="(-h)" name="h" type="boolean" falsevalue="" truevalue="-h"/>
27 </inputs>
28 <outputs>
29 <data format_source="in_fa1" hidden="false" name="default" label="Merger of $in_fa1.name and $in_fa2.name"/>
30 </outputs>
31 <tests>
32 <test>
33 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
34 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
35 <output name="default" file="seqtk_mergefa.out" ftype="fasta"/>
36 </test>
37 <test>
38 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
39 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
40 <param name="m" value="True" />
41 <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/>
42 </test>
43 </tests>
44 <help><![CDATA[
45 **What it does**
46
47 Merges two fasta files, using ambiguity codes
48
49 ::
50
51 # seq1.fa
52 >test0
53 ACTGACTGAAA
54
55 # seq2.fa
56 >test0
57 ACTGAMTGCGN
58
59 In the following the `-m` option has been set to highlight seqtk-mergefa's features.
60
61 ::
62
63 >test0
64 ACTGACTGxxa
65
66 @ATTRIBUTION@
67 ]]></help>
68 </tool>