Mercurial > repos > iuc > stacks_denovomap

annotate stacks_denovomap.xml @ 0:9d588fb2aee5 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 f3a59c91c231cc1582479109e776d05602b7f24d-dirty
author iuc
date Tue, 14 Jun 2016 14:07:29 -0400
parents
children bab631cc9f64
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
1 <tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.0">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
2 <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
3 <macros>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
4 <import>macros.xml</import>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
5 </macros>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
7 <expand macro="stdio"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
8 <command><![CDATA[
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
9 #from os.path import splitext
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
10 #import re
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
11
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
12 #if str( $options_usage.rad_analysis_type ) == "genetic":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
13 #for $input_parent in $options_usage.parent_sequences:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
14
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
15 #if $input_parent.ext == "fastqsanger":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
16 #set $data_path = splitext($input_parent.name)[0]
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
17 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
18 #set $data_path = $data_path + ".fq"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
19 #else:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
20 #set $data_path = splitext($input_parent.name)[0]
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
21 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
22 #set $data_path = $data_path + ".fa"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
23 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
24
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
25 ln -s "${input_parent}" "${data_path}" &&
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
26 #end for
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
27
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
28 #for $input_progeny in $options_usage.progeny_sequences:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
29
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
30 #if $input_progeny.ext == "fastqsanger":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
31 #set $data_path = splitext($input_progeny.name)[0]
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
32 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
33 #set $data_path = $data_path + ".fq"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
34 #else:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
35 #set $data_path = splitext($input_progeny.name)[0]
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
36 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
37 #set $data_path = $data_path + ".fa"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
38 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
39
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
40 ln -s "${input_progeny}" "${data_path}" &&
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
41 #end for
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
42 #else:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
43 #for $input_indiv in $options_usage.individual_sample:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
44
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
45 #if $input_indiv.ext == "fastqsanger":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
46 #set $data_path = splitext($input_indiv.name)[0]
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
47 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
48 #set $data_path = $data_path + ".fq"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
49 #else:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
50 #set $data_path = splitext($input_indiv.name)[0]
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
51 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
52 #set $data_path = $data_path + ".fa"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
53 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
54
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
55 ln -s "${input_indiv}" "${data_path}" &&
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
56 #end for
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
57 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
58
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
59 mkdir stacks_outputs
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
60
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
61 &&
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
62
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
63 denovo_map.pl
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
64
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
65 -T \${GALAXY_SLOTS:-1}
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
66
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
67 #if str( $options_usage.rad_analysis_type ) == "genetic":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
68 #for $input_parent in $options_usage.parent_sequences:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
69 #if $input_parent.ext == "fastqsanger":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
70 #set $data_path = splitext($input_parent.name)[0]
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
71 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
72 #set $data_path = $data_path + ".fq"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
73 #else:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
74 #set $data_path = splitext($input_parent.name)[0]
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
75 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
76 #set $data_path = $data_path + ".fa"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
77 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
78
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
79 -p "${data_path}"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
80 #end for
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
81
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
82 -A $options_usage.cross_type
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
83
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
84 #for $input_progeny in $options_usage.progeny_sequences:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
85 #if $input_progeny.ext == "fastqsanger":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
86 #set $data_path = splitext($input_progeny.name)[0]
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
87 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
88 #set $data_path = $data_path + ".fq"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
89 #else:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
90 #set $data_path = splitext($input_progeny.name)[0]
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
91 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
92 #set $data_path = $data_path + ".fa"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
93 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
94
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
95 -r "${data_path}"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
96 #end for
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
97
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
98 #if str($assembly_options.P):
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
99 -P $assembly_options.P
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
100 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
101 #else:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
102 #for $i_indiv, $input_indiv in enumerate($options_usage.individual_sample):
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
103
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
104 #if $input_indiv.ext == "fastqsanger":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
105 #set $data_path = splitext($input_indiv.name)[0]
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
106 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
107 #set $data_path = $data_path + ".fq"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
108 #else:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
109 #set $data_path = splitext($input_indiv.name)[0]
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
110 #set $data_path = re.sub(r'\.1$', '', $data_path)
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
111 #set $data_path = $data_path + ".fa"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
112 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
113
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
114 -s "${data_path}"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
115 #end for
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
116 -O "$options_usage.popmap"
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
117 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
118
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
119 #if str($assembly_options.m):
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
120 -m $assembly_options.m
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
121 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
122 #if str($assembly_options.N):
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
123 -N $assembly_options.N
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
124 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
125 -M $assembly_options.M
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
126 -n $assembly_options.n
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
127 -t $assembly_options.t
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
128 -H $assembly_options.H
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
129
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
130 ## Batch description
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
131 -b 1
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
132
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
133 ## No SQL recording
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
134 -S
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
135
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
136 ## snp_model
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
137 #if str( $snp_options.select_model.model_type) == "bounded":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
138 --bound_low $snp_options.select_model.bound_low
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
139 --bound_high $snp_options.select_model.bound_high
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
140 --alpha $snp_options.select_model.alpha
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
141 #else if str( $snp_options.select_model.model_type) == "snp":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
142 --alpha $snp_options.select_model.alpha
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
143 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
144
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
145 -o stacks_outputs
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
146
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
147 #if str( $options_usage.rad_analysis_type ) == "genetic":
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
148 @NORM_GENOTYPES_OUTPUT_LIGHT@
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
149 #end if
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
150 ]]></command>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
151
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
152 <inputs>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
153 <conditional name="options_usage">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
154 <param name="rad_analysis_type" type="select" label="Select your usage">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
155 <option value="genetic" selected="true">Genetic map</option>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
156 <option value="population">Population</option>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
157 </param>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
158 <when value="genetic">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
159 <param name="parent_sequences" argument="-p" format="fastqsanger,fasta" type="data" multiple="true" label="Files containing parent sequences" help="Files containing parent sequences from a mapping cross" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
160
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
161 <param name="progeny_sequences" argument="-r" format="fastqsanger,fasta" type="data" multiple="true" optional="true" label="Files containing progeny sequences" help="files containing progeny sequences from a mapping cross" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
162
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
163 <param name="cross_type" argument="-A" type="select" label="Cross type">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
164 <expand macro="cross_types"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
165 </param>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
166 </when>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
167 <when value="population">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
168 <param name="individual_sample" argument="-s" format="fastqsanger,fasta" type="data" multiple="true" label="Files containing an individual sample from a population" help="files containing an individual sample from a population" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
169 <param name="popmap" argument="-O" type="data" format="tabular,txt" label="Specify a population map" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
170 </when>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
171 </conditional>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
172
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
173 <!-- stack assembly options -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
174 <section name="assembly_options" title="Assembly options" expanded="false">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
175 <param name="m" argument="-m" type="integer" value="" optional="true" label="Minimum number of identical raw reads required to create a stack" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
176 <param name="P" argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
177 <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
178 <param name="N" argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
179 <param name="n" argument="-n" type="integer" value="1" label="specify the number of mismatches allowed between loci when building the catalog"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
180
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
181 <param name="t" argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
182 <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
183 </section>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
184
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
185 <!-- SNP Model options -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
186 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
187 <expand macro="snp_options"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
188 </section>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
189 </inputs>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
190 <outputs>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
191 <data format="txt" name="output_log" label="denovo_map.log with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/denovo_map.log" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
192
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
193 <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
194 <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
195 <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
196
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
197 <expand macro="genotypes_output_light"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
198 <expand macro="populations_output_light"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
199
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
200 <collection name="tags" type="list" label="Assembled loci from ${on_string}">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
201 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
202 </collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
203
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
204 <collection name="snps" type="list" label="Model calls from each locus on ${on_string}">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
205 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
206 </collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
207
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
208 <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus on ${on_string}">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
209 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
210 </collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
211
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
212 <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
213 <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv" ext="tabular" directory="stacks_outputs" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
214 </collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
215
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
216 <collection name="all_output" type="list" label="Full output from denovo_map on ${on_string}">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
217 <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles|matches))\.tsv" ext="tabular" directory="stacks_outputs" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
218 <discover_datasets pattern="(?P&lt;name&gt;.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv" ext="tabular" directory="stacks_outputs" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
219 <discover_datasets pattern="(?P&lt;name&gt;.+\.(genotypes))\.(loc|txt)" ext="txt" directory="stacks_outputs" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
220 </collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
221 </outputs>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
222
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
223 <tests>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
224 <test>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
225 <param name="options_usage|rad_analysis_type" value="genetic"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
226 <param name="options_usage|parent_sequences" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
227 <param name="options_usage|progeny_sequences" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
228 <output name="output_log">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
229 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
230 <has_text text="denovo_map.pl completed" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
231 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
232 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
233
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
234 <!-- catalog -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
235 <output name="catalogtags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
236 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
237 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
238 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
239 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
240 <output name="catalogsnps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
241 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
242 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
243 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
244 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
245 <output name="catalogalleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
246 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
247 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
248 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
249 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
250
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
251 <!-- genotypes -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
252 <output name="out_generic_haplo">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
253 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
254 <has_text text="Catalog ID" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
255 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
256 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
257 <output name="out_sql_markers">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
258 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
259 <has_text text="Total Genotypes" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
260 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
261 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
262 <output name="out_joinmap">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
263 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
264 <has_text text="batch_1.genotypes_" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
265 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
266 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
267 <output name="out_sql_genotypes">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
268 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
269 <has_text text="SQL ID" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
270 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
271 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
272
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
273 <!-- samples -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
274 <output_collection name="tags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
275 <element name="PopA_01.tags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
276 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
277 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
278 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
279 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
280 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
281 <output_collection name="snps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
282 <element name="PopA_01.snps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
283 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
284 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
285 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
286 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
287 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
288 <output_collection name="alleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
289 <element name="PopA_01.alleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
290 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
291 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
292 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
293 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
294 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
295 <output_collection name="matches">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
296 <element name="PopA_01.matches">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
297 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
298 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
299 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
300 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
301 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
302 </test>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
303 <test>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
304 <param name="options_usage|rad_analysis_type" value="population"/>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
305 <param name="options_usage|individual_sample" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq,demultiplexed/PopA_03.1.fq,demultiplexed/PopA_04.1.fq,demultiplexed/PopB_01.1.fq,demultiplexed/PopB_02.1.fq,demultiplexed/PopB_03.1.fq,demultiplexed/PopB_04.1.fq" ftype="fastqsanger" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
306 <param name="options_usage|popmap" value="denovo_map/popmap.tsv" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
307 <output name="output_log">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
308 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
309 <has_text text="denovo_map.pl completed" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
310 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
311 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
312
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
313 <!-- catalog -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
314 <output name="catalogtags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
315 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
316 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
317 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
318 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
319 <output name="catalogsnps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
320 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
321 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
322 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
323 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
324 <output name="catalogalleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
325 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
326 <has_text text="catalog generated on" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
327 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
328 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
329
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
330 <!-- populations -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
331 <output name="out_haplotypes">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
332 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
333 <has_text text="PopA_01" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
334 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
335 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
336 <output name="out_hapstats">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
337 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
338 <has_text text="Smoothed Gene Diversity" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
339 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
340 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
341 <output name="out_populations_log">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
342 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
343 <has_text text="populations version" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
344 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
345 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
346 <output name="out_sumstats_sum">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
347 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
348 <has_text text="Polymorphic Sites" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
349 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
350 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
351 <output name="out_sumstats">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
352 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
353 <has_text text="Smoothed Pi" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
354 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
355 </output>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
356
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
357 <!-- samples -->
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
358 <output_collection name="tags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
359 <element name="PopA_01.tags">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
360 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
361 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
362 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
363 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
364 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
365 <output_collection name="snps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
366 <element name="PopA_01.snps">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
367 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
368 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
369 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
370 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
371 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
372 <output_collection name="alleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
373 <element name="PopA_01.alleles">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
374 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
375 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
376 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
377 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
378 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
379 <output_collection name="matches">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
380 <element name="PopA_01.matches">
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
381 <assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
382 <has_text text="generated on " />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
383 </assert_contents>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
384 </element>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
385 </output_collection>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
386 </test>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
387 </tests>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
388
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
389 <help>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
390 <![CDATA[
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
391 .. class:: infomark
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
392
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
393 **What it does**
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
394
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
395 This program will run each of the Stacks components: first, running ustacks on each of the samples specified, building loci and calling SNPs in each. Second, cstacks will be run to create a catalog of all loci that were marked as 'parents' or 'samples' on the command line, and finally, sstacks will be executed to match each sample against the catalog. A bit more detail on this process can be found in the FAQ. The denovo_map.pl program will also load the results of each stage of the analysis: individual loci, the catalog, and matches against the catalog into the database (although this can be disabled). After matching, the program will build a database index to speed up access (index_radtags.pl) and enable web-based filtering.
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
396
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
397 --------
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
398
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
399 **Input files**
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
400
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
401 FASTQ, FASTA
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
402
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
403 - Population map::
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
404
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
405 indv_01 1
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
406 indv_02 1
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
407 indv_03 1
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
408 indv_04 2
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
409 indv_05 2
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
410 indv_06 2
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
411
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
412
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
413 **Output files**
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
414
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
415
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
416 - XXX.tags.tsv file:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
417
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
418 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
419
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
420 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
421
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
422
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
423 - XXX.snps.tsv file:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
424
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
425 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
426
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
427 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
428
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
429
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
430 - XXX.alleles.tsv file:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
431
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
432 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
433
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
434
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
435 - XXX.matches.tsv file:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
436
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
437 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
438
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
439 Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample.
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
440
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
441
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
442 - other files:
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
443
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
444 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
445
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
446 @STACKS_INFOS@
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
447 ]]>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
448 </help>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
449 <expand macro="citation" />
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
450 </tool>
9d588fb2aee5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
451