Mercurial > repos > iuc > data_manager_bwameth_index_builder
changeset 2:0beac6016b41 draft
"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 | 2ee9ab762320 |
| children | d1c0b1f0c67e |
| files | data_manager/bwameth_index_builder.py data_manager/bwameth_index_builder.xml data_manager_conf.xml tool_dependencies.xml |
| diffstat | 4 files changed, 30 insertions(+), 44 deletions(-) [+] |
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--- a/data_manager/bwameth_index_builder.py Tue Apr 04 17:49:45 2017 -0400 +++ b/data_manager/bwameth_index_builder.py Tue Oct 01 17:52:30 2019 -0400 @@ -24,7 +24,7 @@ if return_code: print >> sys.stderr, "Error building index." sys.exit( return_code ) - data_table_entry = dict(value=args.dbKey, dbkey=args.dbkey, name=args.name, path=args.dbKey) + data_table_entry = dict(value=args.dbkey, dbkey=args.dbkey, name=args.name, path=sym_linked_fasta_filename) _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
--- a/data_manager/bwameth_index_builder.xml Tue Apr 04 17:49:45 2017 -0400 +++ b/data_manager/bwameth_index_builder.xml Tue Oct 01 17:52:30 2019 -0400 @@ -1,53 +1,51 @@ -<tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0"> +<tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0.1"> <description>builder</description> + <macros> + <token name="@TOOL_VERSION@">0.2.2</token> + </macros> <requirements> - <requirement type="package" version="0.7.12">bwa</requirement> - <requirement type="package" version="1.2">samtools</requirement> - <requirement type="package" version="0.2.0">bwameth</requirement> + <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[ - #if str($sequence_id).strip() != "": - #set $dbkey = $sequence_id - #else: - #set $dbkey = $all_fasta_source.fields.dbkey - #end if +#if str($sequence_id).strip(): + #set $dbkey = $sequence_id +#else: + #set $dbkey = $all_fasta_source.fields.dbkey +#end if - #if str($sequence_name).strip() != "": - #set $name = $sequence_name - #else: - #set $name = $all_fasta_source.fields.name - #end if +#if str($sequence_name).strip(): + #set $name = $sequence_name +#else: + #set $name = $all_fasta_source.fields.name +#end if - python $__tool_directory__/bwameth_index_builder.py --output "${out_file}" - --fasta_filename "${all_fasta_source.fields.path}" - --dbkey "${dbkey}" - --name "${name}" - --data_table_name "bwameth_indexes" - ]]> - </command> +python '$__tool_directory__/bwameth_index_builder.py' --output '${out_file}' +--fasta_filename '${all_fasta_source.fields.path}' +--dbkey '${dbkey}' +--name '${name}' +--data_table_name bwameth_indexes + ]]></command> <inputs> - <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> + <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> <options from_data_table="all_fasta" /> </param> - <param label="ID for index" name="sequence_id" type="text" value="" help="If not specified, the value from the fasta file is used"/> - <param label="Displayed description for sequence" name="sequence_name" type="text" value="" help="If not specified, the value from the fasta file is used"/> + <param name="sequence_id" type="text" value="" label="ID for index" help="If not specified, the value from the fasta file is used"/> + <param name="sequence_name" type="text" value="" label="Displayed description for sequence" help="If not specified, the value from the fasta file is used"/> </inputs> <outputs> - <data format="data_manager_json" name="out_file" /> + <data name="out_file" format="data_manager_json" /> </outputs> - <help> -<![CDATA[ + <help><![CDATA[ .. class:: infomark -**Notice:** If you leave name, description, or id blank, it will be generated automatically. +**Notice:** If you leave name, description, or id blank, it will be generated automatically. What is BWA-meth? ----------------- 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. -]]> - </help> + ]]></help> <citations> <citation type="bibtex">@misc{1401.1129, Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
--- a/data_manager_conf.xml Tue Apr 04 17:49:45 2017 -0400 +++ b/data_manager_conf.xml Tue Oct 01 17:52:30 2019 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager/bwameth_index_builder.xml" id="bwameth_index_builder" version="0.0.1"> + <data_manager tool_file="data_manager/bwameth_index_builder.xml" id="bwameth_index_builder"> <data_table name="bwameth_indexes"> <output> <column name="value" />
--- a/tool_dependencies.xml Tue Apr 04 17:49:45 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bwa" version="0.7.12"> - <repository changeset_revision="67aa12c8d449" name="package_bwa_0_7_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="1.2"> - <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="bwameth" version="0.2.0"> - <repository changeset_revision="fd470f9ef129" name="package_python_2_7_bwameth_0_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>