0
|
1 <tool id="bsf-call" name="bsf-call" version="1.0.0">
|
|
2 <description>Mapping bisulfite-seq reads and calling methylated cytosines</description>
|
|
3 <!--
|
|
4 <version_command></version_command>
|
|
5 -->
|
|
6
|
|
7 <requirements>
|
|
8 <requirement type="set_environment">TOOLDIR</requirement>
|
|
9 </requirements>
|
|
10
|
|
11 <command interpreter="perl">
|
|
12 bsf-call_wrapper.pl TOOLDIR $reference.source $read.end \${GALAXY_SLOTS:-1}
|
|
13
|
|
14 #if $reference.source=="indexed":
|
|
15 $reference.index.fields.path
|
|
16 #else if $reference.source=="history":
|
|
17 $reference.own_file
|
|
18 #else
|
|
19
|
|
20 #end if
|
|
21
|
|
22 #if $read.end=="single-end"
|
|
23 $in
|
|
24 #else if $read.end=="paired-end"
|
|
25 $in1 $in2
|
|
26 #else
|
|
27
|
|
28 #end if
|
|
29 </command>
|
|
30
|
|
31 <inputs>
|
|
32 <conditional name="reference">
|
|
33 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?">
|
|
34 <option value="indexed">Use a built-in genome index</option>
|
|
35 <option value="history">Use a genome from the history and build index</option>
|
|
36 </param>
|
|
37 <when value="indexed">
|
|
38 <param name="index" type="select" label="Select reference genome">
|
|
39 <options from_data_table="bsf-call_indexes">
|
|
40 <filter type="sort_by" column="2"/>
|
|
41 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
|
|
42 </options>
|
|
43 </param>
|
|
44 </when>
|
|
45 <when value="history">
|
|
46 <param name="own_file" type="data" format="fasta" label="Select reference genome"/>
|
|
47 </when>
|
|
48 </conditional>
|
|
49
|
|
50 <conditional name="read">
|
|
51 <param name="end" type="select" label="Will you use single-end reads or paired-end reads?">
|
|
52 <option value="single-end">Single-end reads</option>
|
|
53 <option value="paired-end">Paired-end reads</option>
|
|
54 </param>
|
|
55 <when value="single-end">
|
|
56 <param name="in" type="data" format="fastqsanger" label="Single-end reads in fastqsanger format"/>
|
|
57 </when>
|
|
58 <when value="paired-end">
|
|
59 <param name="in1" type="data" format="fastqsanger" label="Paired-end reads 1 in fastqsanger format"/>
|
|
60 <param name="in2" type="data" format="fastqsanger" label="Paired-end reads 2 in fastqsanger format"/>
|
|
61 </when>
|
|
62 </conditional>
|
|
63 </inputs>
|
|
64
|
|
65 <outputs>
|
|
66 <data name="outres" format="tabular" label="${tool.name} on ${on_string}: result" from_work_dir="bsf-call.out"/>
|
|
67 <data name="outlog" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="bsfwork/bsf-call.log"/>
|
|
68 </outputs>
|
|
69
|
|
70 <help>
|
|
71 **bsf-call**
|
|
72
|
|
73 Mapping bisulfite-seq reads and calling methylated cytosines
|
|
74
|
|
75 ------
|
|
76
|
|
77 **Input format**
|
|
78
|
|
79 Inputs are bisulfite-seq reads in fastqsanger format (single-end or paired-end), and a reference genome index (built-in or constructed from your fasta file).
|
|
80
|
|
81 ------
|
|
82
|
|
83 **Output format**
|
|
84
|
|
85 Output is a six-column tab-delimited file::
|
|
86
|
|
87 Col.| Description
|
|
88 ----+--------------------------------------
|
|
89 1 | chromosome label (e.g. chr1)
|
|
90 2 | genomic position (0-based)
|
|
91 3 | strand (+,-)
|
|
92 4 | mC context (CG, CHG, CHH)
|
|
93 5 | mC rate (float)
|
|
94 6 | read coverage
|
|
95
|
|
96 ------
|
|
97
|
|
98 **Contact**
|
|
99
|
|
100 Toutai Mituyama
|
|
101
|
|
102 mituyama-toutai AT aist.go.jp
|
|
103 </help>
|
|
104
|
|
105 <citations>
|
|
106 <citation type="doi">10.1093/nar/gkt1373</citation>
|
|
107 </citations>
|
|
108
|
|
109 </tool>
|
|
110
|
|
111 <!--
|
|
112 Also note the use of the reserved parameter name GALAXY_DATA_INDEX_DIR - it points to the ~/tool-data directory.
|
|
113 \${GALAXY_SLOTS:-4}
|
|
114
|
|
115 Number of cores/threads allocated by the job runner or resource manager to the tool for the given job (here 4 is the default number of threads to use if running via custom runner that does not configure GALAXY_SLOTS or in an older Galaxy runtime).
|
|
116 -->
|