Mercurial > repos > iuc > data_manager_bwameth_index_builder
comparison data_manager/bwameth_index_builder.xml @ 0:fa17303fc8de draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 30192223eeb60f33a42046921351c6ba3c80c90c
| author | iuc |
|---|---|
| date | Tue, 22 Nov 2016 17:11:42 -0500 |
| parents | |
| children | 0beac6016b41 |
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| -1:000000000000 | 0:fa17303fc8de |
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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> |