Mercurial > repos > iuc > data_manager_bwameth_index_builder

annotate data_manager/bwameth_index_builder.xml @ 5:f95ae6d21db4 draft default tip

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 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:42:43 +0000
parents ecd6bdddcdec
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
ecd6bdddcdec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents: 2
diff changeset
1 <tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0.2" profile="18.09">
0
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
2 <description>builder</description>
2
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
3 <macros>
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
4 <token name="@TOOL_VERSION@">0.2.2</token>
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
5 </macros>
0
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
6 <requirements>
2
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement>
0
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
8 </requirements>
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
9 <command detect_errors="aggressive"><![CDATA[
2
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
10 #if str($sequence_id).strip():
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
11 #set $dbkey = $sequence_id
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
12 #else:
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
13 #set $dbkey = $all_fasta_source.fields.dbkey
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
14 #end if
0
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
15
2
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
16 #if str($sequence_name).strip():
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
17 #set $name = $sequence_name
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
18 #else:
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
19 #set $name = $all_fasta_source.fields.name
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
20 #end if
0
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
21
2
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
22 python '$__tool_directory__/bwameth_index_builder.py' --output '${out_file}'
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
23 --fasta_filename '${all_fasta_source.fields.path}'
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
24 --dbkey '${dbkey}'
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
25 --name '${name}'
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
26 --data_table_name bwameth_indexes
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
27 ]]></command>
0
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
28 <inputs>
2
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
29 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
0
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
30 <options from_data_table="all_fasta" />
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
31 </param>
2
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
32 <param name="sequence_id" type="text" value="" label="ID for index" help="If not specified, the value from the fasta file is used"/>
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
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"/>
0
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
34 </inputs>
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
35 <outputs>
4
ecd6bdddcdec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents: 2
diff changeset
36 <data name="out_file" format="data_manager_json"/>
0
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
37 </outputs>
4
ecd6bdddcdec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents: 2
diff changeset
38 <tests>
ecd6bdddcdec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents: 2
diff changeset
39 <test>
ecd6bdddcdec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents: 2
diff changeset
40 <param name="all_fasta_source" value="phiX174"/>
ecd6bdddcdec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents: 2
diff changeset
41 <output name="out_file" value="bwameth_data_manager.json" compare="re_match"/>
ecd6bdddcdec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents: 2
diff changeset
42 </test>
ecd6bdddcdec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
iuc
parents: 2
diff changeset
43 </tests>
2
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
44 <help><![CDATA[
0
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
45 .. class:: infomark
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
46
2
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
47 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
0
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
48
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
49 What is BWA-meth?
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
50 -----------------
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
51
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
52 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.
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
53
2
0beac6016b41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"
iuc
parents: 0
diff changeset
54 ]]></help>
0
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
55 <citations>
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
56 <citation type="bibtex">@misc{1401.1129,
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
57 Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
58 Title = {Fast and accurate alignment of long bisulfite-seq reads},
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
59 Year = {2014},
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
60 Eprint = {arXiv:1401.1129},
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
61 }</citation>
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
62 </citations>
fa17303fc8de planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
iuc
parents:
diff changeset
63 </tool>