Mercurial > repos > iuc > data_manager_bwameth_index_builder
comparison data_manager/bwameth_index_builder.xml @ 4:a9aa093e2392 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
author | iuc |
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date | Tue, 01 Oct 2019 17:53:16 -0400 |
parents | a7fb84abef45 |
children | 5ab25caa7b7d |
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3:e7ca32457e36 | 4: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"> | 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}, |