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comparison seqtk_mergefa.xml @ 3:bc7d99f46a5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author iuc
date Mon, 05 Jun 2017 13:27:11 -0400
parents f73729b62b51
children ecf1c30da3a2
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2:f73729b62b51 3:bc7d99f46a5d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="seqtk_mergefa" name="seqtk_mergefa" version="@WRAPPER_VERSION@.0"> 2 <tool id="seqtk_mergefa" name="seqtk_mergefa" version="@WRAPPER_VERSION@.0">
3 <description>merge two FASTA/Q files</description> 3 <description>merge two FASTA/Q files</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[seqtk mergefa -q $q 9 <command><![CDATA[
10 seqtk mergefa
11 -q $q
10 $i 12 $i
11 $m 13 $m
12 $r 14 $r
13 $h 15 $h
14 16 '$in_fa1'
15 $in_fa1 17 '$in_fa2'
16 $in_fa2 18 > '$default'
17 19 ]]></command>
18 > $default]]></command> 20 <inputs>
19 <inputs> 21 <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
20 <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/> 22 <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
21 <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/> 23 <param argument="-q" type="integer" value="0" label="Quality threshold"/>
22 <param label="quality threshold" help="(-q)" name="q" type="integer" value="0"/> 24 <param argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Take intersection" />
23 <param checked="false" label="take intersection" help="(-i)" name="i" type="boolean" falsevalue="" truevalue="-i"/> 25 <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Convert to lowercase when one of the input base is N" />
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"/> 26 <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Pick a random allele from het" />
25 <param checked="false" label="pick a random allele from het" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/> 27 <param argument="-h" type="boolean" truevalue="-h" falsevalue="" checked="false" label="Suppress hets in the input" />
26 <param checked="false" label="suppress hets in the input" help="(-h)" name="h" type="boolean" falsevalue="" truevalue="-h"/> 28 </inputs>
27 </inputs> 29 <outputs>
28 <outputs> 30 <data name="default" format_source="in_fa1" label="Merger of $in_fa1.name and $in_fa2.name"/>
29 <data format_source="in_fa1" hidden="false" name="default" label="Merger of $in_fa1.name and $in_fa2.name"/> 31 </outputs>
30 </outputs> 32 <tests>
31 <tests> 33 <test>
32 <test> 34 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
33 <param name="in_fa1" value="seqtk_mergefa1.fa"/> 35 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
34 <param name="in_fa2" value="seqtk_mergefa2.fa"/> 36 <output name="default" file="seqtk_mergefa.out" ftype="fasta"/>
35 <output name="default" file="seqtk_mergefa.out" ftype="fasta"/> 37 </test>
36 </test> 38 <test>
37 <test> 39 <param name="in_fa1" value="seqtk_mergefa1.fa"/>
38 <param name="in_fa1" value="seqtk_mergefa1.fa"/> 40 <param name="in_fa2" value="seqtk_mergefa2.fa"/>
39 <param name="in_fa2" value="seqtk_mergefa2.fa"/> 41 <param name="m" value="True" />
40 <param name="m" value="True" /> 42 <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/>
41 <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/> 43 </test>
42 </test> 44 </tests>
43 </tests> 45 <help><![CDATA[
44 <help><![CDATA[
45 **What it does** 46 **What it does**
46 47
47 Merges two fasta files, using ambiguity codes 48 Merges two fasta files, using ambiguity codes
48 49
49 :: 50 ::
62 63
63 >test0 64 >test0
64 ACTGACTGxxa 65 ACTGACTGxxa
65 66
66 @ATTRIBUTION@ 67 @ATTRIBUTION@
67 ]]></help> 68 ]]></help>
68 <expand macro="citation" /> 69 <expand macro="citation" />
69 </tool> 70 </tool>