Mercurial > repos > iuc > data_manager_bwameth_index_builder
comparison data_manager/bwameth_index_builder.xml @ 0:a7fb84abef45 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
author | iuc |
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date | Tue, 22 Nov 2016 17:12:00 -0500 |
parents | |
children | a9aa093e2392 |
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1 <tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0"> | |
2 <description>builder</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.7.12">bwa</requirement> | |
5 <requirement type="package" version="1.2">samtools</requirement> | |
6 <requirement type="package" version="0.2.0">bwameth</requirement> | |
7 </requirements> | |
8 <command detect_errors="aggressive"><![CDATA[ | |
9 #if str($sequence_id).strip() != "": | |
10 #set $dbkey = $sequence_id | |
11 #else: | |
12 #set $dbkey = $all_fasta_source.fields.dbkey | |
13 #end if | |
14 | |
15 #if str($sequence_name).strip() != "": | |
16 #set $name = $sequence_name | |
17 #else: | |
18 #set $name = $all_fasta_source.fields.name | |
19 #end if | |
20 | |
21 python $__tool_directory__/bwameth_index_builder.py --output "${out_file}" | |
22 --fasta_filename "${all_fasta_source.fields.path}" | |
23 --dbkey "${dbkey}" | |
24 --name "${name}" | |
25 --data_table_name "bwameth_indexes" | |
26 ]]> | |
27 </command> | |
28 <inputs> | |
29 <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> | |
30 <options from_data_table="all_fasta" /> | |
31 </param> | |
32 <param label="ID for index" name="sequence_id" type="text" value="" help="If not specified, the value from the fasta file is used"/> | |
33 <param label="Displayed description for sequence" name="sequence_name" type="text" value="" help="If not specified, the value from the fasta file is used"/> | |
34 </inputs> | |
35 <outputs> | |
36 <data format="data_manager_json" name="out_file" /> | |
37 </outputs> | |
38 <help> | |
39 <![CDATA[ | |
40 .. class:: infomark | |
41 | |
42 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
43 | |
44 What is BWA-meth? | |
45 ----------------- | |
46 | |
47 BWA-meth performs alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. The methodology employed for this is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool. | |
48 | |
49 ]]> | |
50 </help> | |
51 <citations> | |
52 <citation type="bibtex">@misc{1401.1129, | |
53 Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz}, | |
54 Title = {Fast and accurate alignment of long bisulfite-seq reads}, | |
55 Year = {2014}, | |
56 Eprint = {arXiv:1401.1129}, | |
57 }</citation> | |
58 </citations> | |
59 </tool> |