Mercurial > repos > iuc > stacks_procrad

annotate stacks_procrad.xml @ 1:a67dae0b1327 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
author iuc
date Mon, 26 Sep 2016 11:42:32 -0400
parents 1dec7bd94bb3
children ba12012b4984
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
a67dae0b1327 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
parents: 0
diff changeset
1 <tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.0">
0
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
2 <description>the Stacks demultiplexing script</description>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
3 <macros>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
4 <import>macros.xml</import>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
5 </macros>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
7 <expand macro="stdio"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
8 <command><![CDATA[
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
9
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
10 #if $input_type.options_type_selector == "single":
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
11
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
12 #if $input_type.input_single.is_of_type('fastqsanger'):
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
13 #set $ext = ".fq"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
14 #set inputype = "fastq"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
15 #else:
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
16 #set $ext = ".fq.gz"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
17 #set inputype = "gzfastq"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
18 #end if
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
19
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
20 ln -s "$input_type.input_single" R1$ext &&
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
21 #else
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
22
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
23 #if $input_type.inputs_paired1.is_of_type('fastqsanger'):
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
24 #set $ext = ".fq"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
25 #set inputype = "fastq"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
26 #else:
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
27 #set $ext = ".fq.gz"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
28 #set inputype = "gzfastq"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
29 #end if
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
30
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
31 ln -s "$input_type.inputs_paired1" R1$ext &&
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
32 ln -s "$input_type.inputs_paired2" R2$ext &&
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
33 #end if
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
34
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
35 mkdir stacks_outputs
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
36
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
37 &&
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
38
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
39 process_radtags
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
40
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
41 #if $input_type.options_type_selector == "single":
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
42 -f R1$ext
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
43 #else:
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
44 -1 R1$ext
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
45 -2 R2$ext
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
46 #end if
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
47
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
48 -i $inputype
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
49 -b "$barcode"
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
50
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
51 $input_type.barcode_encoding
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
52
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
53 #if str( $options_enzyme.options_enzyme_selector ) == "1":
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
54 -e $options_enzyme.enzyme
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
55 #else:
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
56 --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
57 #end if
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
58
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
59 -y $outype
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
60
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
61 $capture
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
62
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
63 #if str($options_advanced.truncate):
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
64 -t $options_advanced.truncate
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
65 #end if
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
66
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
67 -w $options_advanced.sliding
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
68
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
69 $options_advanced.remove
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
70
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
71 $options_advanced.discard
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
72 -s $options_advanced.score
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
73
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
74 $options_advanced.rescue
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
75
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
76 -o stacks_outputs
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
77 ]]></command>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
78
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
79 <inputs>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
80 <conditional name="input_type">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
81 <param name="options_type_selector" type="select" label="Single-end or paired-end reads files">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
82 <option value="single" selected="True">Single-end files</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
83 <option value="paired">Paired-end files</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
84 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
85 <when value="single">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
86 <param name="input_single" argument="-f" format="fastqsanger,fastq.gz" type="data" label="singles-end reads infile(s)" help="input files" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
87
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
88 <param name="barcode_encoding" type="select" label="Barcode location">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
89 <option value="--inline_null" selected="True">Barcode is inline with sequence</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
90 <option value="--index_null">Barcode is provided in FASTQ header</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
91 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
92 </when>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
93 <when value="paired">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
94 <param name="inputs_paired1" argument="-1" format="fastqsanger,fastq.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
95 <param name="inputs_paired2" argument="-2" format="fastqsanger,fastq.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
96
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
97 <param name="barcode_encoding" type="select" label="Barcode location">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
98 <option value="--inline_null" selected="True">Barcode is inline with sequence, only on the single-end read (read 1)</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
99 <option value="--index_null">Barcode is provided in FASTQ header, only on the single-end read (read 1)</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
100 <option value="--inline_inline">Barcode is inline with sequence, on both single and paired-end read (read 1 and 2)</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
101 <option value="--index_index">Barcode is provided in FASTQ header, on both single and paired-end read (read 1 and 2)</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
102 <option value="--inline_index">Barcode is inline with sequence on single-end read (read 1), and in FASTQ header for paired-end read (read 2)</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
103 <option value="--index_inline">Barcode is provided in FASTQ header on single-end read (read 1), and is inline with sequence on paired-end read (read 2)</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
104 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
105 </when>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
106 </conditional>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
107
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
108 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" help="Barcode file" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
109
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
110 <conditional name="options_enzyme">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
111 <param name="options_enzyme_selector" type="select" label="Number of enzymes">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
112 <option value="1">One</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
113 <option value="2">Two</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
114 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
115 <when value="1">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
116 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" >
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
117 <expand macro="enzymes"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
118 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
119 </when>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
120 <when value="2">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
121 <param name="enzyme" type="select" label="Enzyme" argument="--renz_1" help="provide the restriction enzyme used" >
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
122 <expand macro="enzymes"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
123 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
124 <param name="enzyme2" type="select" label="Second enzyme" argument="--renz_2" help="provide the second restriction enzyme used" >
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
125 <expand macro="enzymes"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
126 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
127 </when>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
128 </conditional>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
129
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
130 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
131
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
132 <section name="options_advanced" title="advanced options" expanded="False">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
133 <param name="sliding" type="float" value="0.15" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15)" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
134 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
135 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
136 <param name="score" type="integer" value="10" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10)" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
137 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
138 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
139 </section>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
140
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
141 <!-- Stacks can produce fastq.gz and fasta.gz output but we don't propose it as they are not very common datatypes in galaxy -->
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
142 <param name="outype" argument="-y" type="select" label="Output format" help="output type, either 'fastq' or 'fasta'" >
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
143 <option value="fastq" selected="True">fastq</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
144 <option value="fasta">fasta</option>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
145 </param>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
146 </inputs>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
147
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
148 <outputs>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
149 <data format="txt" name="output_log" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" from_work_dir="stacks_outputs/process_radtags.log" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
150
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
151 <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
152 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
153 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
154 </collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
155 <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
156 <filter>input_type['options_type_selector'] == "paired"</filter>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
157 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
158 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
159 </collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
160 <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
161 <filter>capture is True</filter>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
162 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
163 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
164 </collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
165 </outputs>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
166
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
167 <tests>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
168 <test>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
169 <param name="options_type_selector" value="single"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
170 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
171 <param name="barcode" value="procrad/barcodes"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
172 <param name="options_enzyme_selector" value="1"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
173 <param name="enzyme" value="ecoRI"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
174 <param name="discard" value="true"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
175 <param name="capture" value="true"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
176 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
177 <output_collection name="demultiplexed">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
178 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
179 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
180 <output_collection name="discarded">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
181 <element name="R1">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
182 <assert_contents>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
183 <has_text text="lane1_fakedata0_11" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
184 </assert_contents>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
185 </element>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
186 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
187 </test>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
188 <test>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
189 <param name="options_type_selector" value="paired"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
190 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
191 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
192 <param name="barcode" value="procrad/barcodes"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
193 <param name="options_enzyme_selector" value="1"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
194 <param name="enzyme" value="ecoRI"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
195 <param name="discard" value="true"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
196 <param name="capture" value="true"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
197 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
198 <output_collection name="demultiplexed">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
199 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
200 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
201 <output_collection name="remaining">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
202 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
203 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
204 <output_collection name="discarded">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
205 <element name="R1">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
206 <assert_contents>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
207 <has_text text="lane1_fakedata0_11" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
208 </assert_contents>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
209 </element>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
210 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
211 </test>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
212 <test>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
213 <param name="options_type_selector" value="paired"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
214 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
215 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
216 <param name="barcode" value="procrad/barcodes"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
217 <param name="options_enzyme_selector" value="1"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
218 <param name="enzyme" value="ecoRI"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
219 <param name="discard" value="true"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
220 <param name="capture" value="true"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
221 <param name="outype" value="fasta"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
222 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
223 <output_collection name="demultiplexed">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
224 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fa"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
225 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
226 <output_collection name="remaining">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
227 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fa"/>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
228 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
229 <output_collection name="discarded">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
230 <element name="R1">
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
231 <assert_contents>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
232 <has_text text="lane1_fakedata0_11" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
233 </assert_contents>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
234 </element>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
235 </output_collection>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
236 </test>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
237 </tests>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
238
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
239
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
240
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
241 <help>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
242 <![CDATA[
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
243 .. class:: infomark
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
244
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
245 **What it does**
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
246
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
247 This program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cutsite are intact, and demultiplexes the data. If there are errors in the barcode or the RAD site within a certain allowance process_radtags can correct them. Second, it slides a window down the length of the read and checks the average quality score within the window. If the score drops below 90% probability of being correct (a raw phred score of 10), the read is discarded. This allows for some seqeuncing errors while elimating reads where the sequence is degrading as it is being sequenced. By default the sliding window is 15% of the length of the read, but can be specified on the command line (the threshold and window size can be adjusted).
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
248
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
249 The process_radtags program can:
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
250
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
251 - handle data that is barcoded, either inline or using an index, or unbarcoded.
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
252 - use combinatorial barcodes.
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
253 - check and correct for a restriction enzyme cutsite for single or double-digested data.
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
254 - filter adapter sequence while allowing for sequencing error in the adapter pattern.
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
255 - process individual files or whole directories of files.
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
256 - directly read gzipped data
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
257 - filter reads based on Illumina's Chastity filter
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
258
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
259 **Help**
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
260
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
261 Input files:
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
262
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
263 - FASTQ
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
264
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
265 - Barcode File Format
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
266
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
267 The barcode file is a very simple format:
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
268
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
269 ======= ===========
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
270 Barcode Sample name
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
271 ======= ===========
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
272 ATGGGG PopA_01
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
273 GGGTAA PopA_02
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
274 AGGAAA PopA_03
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
275 TTTAAG PopA_04
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
276 GGTGTG PopA_05
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
277 TGATGT PopA_06
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
278 ======= ===========
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
279
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
280 Combinatorial barcodes are specified, one per column, separated by a tab:
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
281
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
282 ======== ======== ===========
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
283 Barcode1 Barcode2 Sample name
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
284 ======== ======== ===========
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
285 CGATA ACGTA PopA_01
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
286 CGGCG CGTA PopA_02
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
287 GAAGC CGTA PopA_03
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
288 GAGAT CGTA PopA_04
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
289 CGATA AGCA PopA_05
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
290 CGGCG AGCA PopA_06
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
291 ======== ======== ===========
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
292
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
293 @STACKS_INFOS@
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
294 ]]>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
295 </help>
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
296 <expand macro="citation" />
1dec7bd94bb3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents:
diff changeset
297 </tool>