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comparison seqtk_subseq.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
comparison
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2:f73729b62b51 3:bc7d99f46a5d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="seqtk_subseq" name="seqtk_subseq" version="@WRAPPER_VERSION@.0"> 2 <tool id="seqtk_subseq" name="seqtk_subseq" version="@WRAPPER_VERSION@.0">
3 <description>extract subsequences from FASTA/Q files</description> 3 <description>extract subsequences from 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 subseq $t 9 <command><![CDATA[
10 seqtk subseq
11 $t
10 -l $l 12 -l $l
11 $in_file 13 '$in_file'
12
13 #if $source.type == 'bed': 14 #if $source.type == 'bed':
14 $in_bed 15 '$in_bed'
15 #else 16 #else
16 $name_list 17 '$name_list'
17 #end if 18 #end if
18
19 #if $t == '-t': 19 #if $t == '-t':
20 | awk 'BEGIN{print "chr\tunknown\tseq"}1' 20 | awk 'BEGIN{print "chr\tunknown\tseq"}1'
21 #end if 21 #end if
22 22 > '$default'
23 > $default]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <param name="in_file" type="data" format="fasta,fastq" label="Input fasta/q file"/> 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">
28 <option value="bed">BED</option> 28 <option value="bed">BED</option>
29 <option value="name">FASTA/Q ID list</option> 29 <option value="name">FASTA/Q ID list</option>
30 </param> 30 </param>
31 <when value="bed"> 31 <when value="bed">
32 <param name="in_bed" type="data" format="bed" label="Input BED file"/> 32 <param name="in_bed" type="data" format="bed" label="Input BED file"/>
33 </when> 33 </when>
34 <when value="name"> 34 <when value="name">
35 <param name="name_list" type="data" format="txt" label="Input fasta file"/> 35 <param name="name_list" type="data" format="txt" label="Input ID list"/>
36 </when> 36 </when>
37 </conditional> 37 </conditional>
38 <param label="TAB delimited output" help="(-t)" name="t" type="boolean" falsevalue="" truevalue="-t"/> 38 <param argument="-t" type="boolean" truevalue="-t" falsevalue="" label="TAB delimited output" />
39 <param label="sequence line length" help="(-l)" name="l" type="integer" value="0"/> 39 <param argument="-l" type="integer" value="0" label="Sequence line length" />
40 </inputs> 40 </inputs>
41 <outputs> 41 <outputs>
42 <data format_source="in_file" hidden="false" name="default" label="Selected sequences from $in_file.name"> 42 <data name="default" format_source="in_file" label="Selected sequences from $in_file.name">
43 <change_format> 43 <change_format>
44 <when input="t" value="-t" format="tabular"/> 44 <when input="t" value="-t" format="tabular"/>
45 </change_format> 45 </change_format>
46 </data> 46 </data>
47 </outputs> 47 </outputs>
48 <tests> 48 <tests>
49 <test> 49 <test>
50 <param name="in_file" value="seqtk_subseq.fa"/> 50 <param name="in_file" value="seqtk_subseq.fa"/>
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 </tests> 56 </tests>
57 <help><![CDATA[ 57 <help><![CDATA[
58 **What it does** 58 **What it does**
59 59
60 Given a list of newline separated IDs from a fasta file, this will extract those named fasta sequences from the input file. 60 Given a list of newline separated IDs from a fasta file, this will extract those named fasta sequences from the input file.
61 61
62 :: 62 ::
77 # Output result 77 # Output result
78 >seq1 78 >seq1
79 ACGTMRWSYK 79 ACGTMRWSYK
80 80
81 @ATTRIBUTION@ 81 @ATTRIBUTION@
82 ]]></help> 82 ]]></help>
83 <expand macro="citation" /> 83 <expand macro="citation" />
84 </tool> 84 </tool>