Mercurial > repos > iuc > data_manager_bwameth_index_builder

comparison data_manager/bwameth_index_builder.xml @ 2:0beac6016b41 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/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
author iuc
date Tue, 01 Oct 2019 17:52:30 -0400
parents fa17303fc8de
children ecd6bdddcdec
comparison
equal deleted inserted replaced
1:2ee9ab762320 2:0beac6016b41
1 <tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0"> 1 <tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0.1">
2 <description>builder</description> 2 <description>builder</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.2.2</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="0.7.12">bwa</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement>
5 <requirement type="package" version="1.2">samtools</requirement>
6 <requirement type="package" version="0.2.0">bwameth</requirement>
7 </requirements> 8 </requirements>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
9 #if str($sequence_id).strip() != "": 10 #if str($sequence_id).strip():
10 #set $dbkey = $sequence_id 11 #set $dbkey = $sequence_id
11 #else: 12 #else:
12 #set $dbkey = $all_fasta_source.fields.dbkey 13 #set $dbkey = $all_fasta_source.fields.dbkey
13 #end if 14 #end if
14 15
15 #if str($sequence_name).strip() != "": 16 #if str($sequence_name).strip():
16 #set $name = $sequence_name 17 #set $name = $sequence_name
17 #else: 18 #else:
18 #set $name = $all_fasta_source.fields.name 19 #set $name = $all_fasta_source.fields.name
19 #end if 20 #end if
20 21
21 python $__tool_directory__/bwameth_index_builder.py --output "${out_file}" 22 python '$__tool_directory__/bwameth_index_builder.py' --output '${out_file}'
22 --fasta_filename "${all_fasta_source.fields.path}" 23 --fasta_filename '${all_fasta_source.fields.path}'
23 --dbkey "${dbkey}" 24 --dbkey '${dbkey}'
24 --name "${name}" 25 --name '${name}'
25 --data_table_name "bwameth_indexes" 26 --data_table_name bwameth_indexes
26 ]]> 27 ]]></command>
27 </command>
28 <inputs> 28 <inputs>
29 <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> 29 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
30 <options from_data_table="all_fasta" /> 30 <options from_data_table="all_fasta" />
31 </param> 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"/> 32 <param name="sequence_id" type="text" value="" label="ID for index" 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"/> 33 <param name="sequence_name" type="text" value="" label="Displayed description for sequence" help="If not specified, the value from the fasta file is used"/>
34 </inputs> 34 </inputs>
35 <outputs> 35 <outputs>
36 <data format="data_manager_json" name="out_file" /> 36 <data name="out_file" format="data_manager_json" />
37 </outputs> 37 </outputs>
38 <help> 38 <help><![CDATA[
39 <![CDATA[
40 .. class:: infomark 39 .. class:: infomark
41 40
42 **Notice:** If you leave name, description, or id blank, it will be generated automatically. 41 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
43 42
44 What is BWA-meth? 43 What is BWA-meth?
45 ----------------- 44 -----------------
46 45
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. 46 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 47
49 ]]> 48 ]]></help>
50 </help>
51 <citations> 49 <citations>
52 <citation type="bibtex">@misc{1401.1129, 50 <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}, 51 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}, 52 Title = {Fast and accurate alignment of long bisulfite-seq reads},
55 Year = {2014}, 53 Year = {2014},