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comparison bsfcall_wrapper.xml @ 1:20930a8f700b

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rename some files
author yutaka-saito
date Sun, 19 Apr 2015 22:39:26 +0900
parents bsf-call_wrapper.xml@06f8460885ff
children f274c166e738
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0:06f8460885ff 1:20930a8f700b
1 <tool id="bsfcall" name="bsfcall" 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 bsfcall_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 $in2
26 #else
27
28 #end if
29 </command>
30
31 <inputs>
32 <conditional name="reference">
33 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?">
34 <option value="indexed">Use a built-in genome index</option>
35 <option value="history">Use a genome from the history and build index</option>
36 </param>
37 <when value="indexed">
38 <param name="index" type="select" label="Select reference genome">
39 <options from_data_table="bsfcall_indexes">
40 <filter type="sort_by" column="2"/>
41 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
42 </options>
43 </param>
44 </when>
45 <when value="history">
46 <param name="own_file" type="data" format="fasta" label="Select reference genome"/>
47 </when>
48 </conditional>
49
50 <conditional name="read">
51 <param name="end" type="select" label="Will you use single-end reads or paired-end reads?">
52 <option value="single-end">Single-end reads</option>
53 <option value="paired-end">Paired-end reads</option>
54 </param>
55 <when value="single-end">
56 <param name="in" type="data" format="fastqsanger" label="Single-end reads in fastqsanger format"/>
57 </when>
58 <when value="paired-end">
59 <param name="in1" type="data" format="fastqsanger" label="Paired-end reads 1 in fastqsanger format"/>
60 <param name="in2" type="data" format="fastqsanger" label="Paired-end reads 2 in fastqsanger format"/>
61 </when>
62 </conditional>
63 </inputs>
64
65 <outputs>
66 <data name="outres" format="tabular" label="${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 -->