Mercurial > repos > yutaka-saito > bsfcall
comparison bsfcall_wrapper.xml @ 1:20930a8f700b
rename some files
author | yutaka-saito |
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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 |
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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 --> |