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planemo upload commit 3ad4270aabe37123987e91a178bd7d61778c849c-dirty
author nml
date Tue, 09 Jan 2018 10:27:22 -0500
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1 <?xml version='1.0' encoding='utf-8'?>
2 <tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.2">
3 <description>Filtering reads or k-mer from fasta file</description>
4 <macros>
5 <token name="@EXECUTABLE@">filter_seq</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="stdio" />
10 <expand macro="version_command" />
11 <command><![CDATA[
12
13
14 cp "$db" db.fasta &&
15
16 #if $single_or_paired.type == "single"
17 ln "$input_se" read.fastq &&
18
19 kat filter seq
20
21 --seq read.fastq
22
23 #elif $single_or_paired.type == "paired"
24 ln "$single_or_paired.forward_pe" read_1.fastq && ln "$single_or_paired.reverse_pe" read_2.fastq &&
25
26 kat filter seq
27
28 --seq read_1.fastq --seq2 read_2.fastq
29
30 #else
31 ln "$single_or_paired.fastq_collection.forward" read_1.fastq && ln "$single_or_paired.fastq_collection.reverse" read_2.fastq &&
32
33 kat filter seq
34
35 --seq read_1.fastq --seq2 read_2.fastq
36
37 #end if
38
39
40 @THREADS@
41
42 --mer_len $kmer
43
44 $stats
45
46 #if $invert_or_both.which == "invert":
47 $invert_or_both.invert
48 #elif $invert_or_both.which == "split":
49 $invert_or_both.separate
50 #end if
51
52 -o reads
53 'db.fasta'
54
55 ]]></command>
56 <inputs>
57 <expand macro="macro_input" />
58
59 <param name="db" type="data" format="fasta" label="Fasta file of targeted regions"/>
60 <expand macro="macro_kmers" />
61
62 <param name="threshold" type="float" value='0.10000000000000001' label="Target Threshold" help="What percentage of the sequence needs to be covered with target k-mers to keep the sequence"/>
63
64 <param name="stats" type="boolean" truevalue='--stats' falsevalue='' checked='False' label="Stats" help="Whether to emit statistics about quantity of found k-mers in each sequence."/>
65 <conditional name="invert_or_both">
66 <param name="which" type="select" label="Advance Options">
67 <option value="none">No Advance</option>
68 <option value="invert">Option 1</option>
69 <option value="split">Option 2</option>
70 </param>
71 <when value="invert">
72 <param name="invert" type="boolean" truevalue='--invert' falsevalue='' checked='True' label="Take k-mer not matching target" help="Whether to take k-mers outside region as selected content, rather than those inside."/>
73 </when>
74 <when value="split">
75 <param name="separate" type="boolean" truevalue='--separate' falsevalue='' checked='True' label="Keep inside and outside of target(s) region" help="Whether to partition the k-mers into two sets, those inside region and those outside."/>
76 </when>
77 <when value="none">
78 </when>
79 </conditional>
80 </inputs>
81 <outputs>
82 <data format="fastqsanger" name="reads" label="Reads.fastq" from_work_dir="reads.in.fastq" >
83 <filter> single_or_paired['type'] == "single" </filter>
84 </data>
85 <data format="fastqsanger" name="forward" label="forward_R1.fastq" from_work_dir="reads.in.R1.fastq" >
86 <filter> single_or_paired['type'] == "paired"</filter>
87 </data>
88 <data format="fastqsanger" name="reverse" label="reverse_R2.fastq" from_work_dir="reads.in.R2.fastq" >
89 <filter> single_or_paired['type'] == "paired"</filter>
90 </data>
91
92
93 <collection name="paired_reads" type="paired" label="Reads">
94 <data name="forward" format="fastqsanger" from_work_dir="reads.in.R1.fastq" >
95 <filter> single_or_paired['type'] == "collection"</filter>
96 </data>
97 <data name="reverse" format="fastqsanger" from_work_dir="reads.in.R2.fastq" >
98 <filter> single_or_paired['type'] == "collection"</filter>
99 </data>
100 </collection>
101
102
103 <data format="fastqsanger" name="outside_reads" label='Outside reads' from_work_dir="reads.out.fastq">
104 <filter>invert_or_both['which'] == 'split' and invert_or_both['separate'] and single_or_paired['type'] == "single"</filter>
105 </data>
106 <data format="tabular" name="file_stats" label='Stats' from_work_dir="reads.stats">
107 <filter>stats</filter>
108 </data>
109
110 </outputs>
111 <tests>
112 <test>
113 <param name="input_se" value="input.fastq" />
114 <param name="db" value="db.fasta" />
115 <output file="matched.fastq" ftype="fastqsanger" name="reads" />
116 </test>
117 </tests>
118 <help><![CDATA[
119 http://kat.readthedocs.io/en/latest/using.html#filtering-tools
120 ]]>
121
122 </help>
123 <citations>
124 </citations>
125 </tool>