| Next changeset 1:404fae08ea31 (2016-12-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit e912b80a0a6a556922a73037843600bd9de687db |
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added:
bwameth.xml test-data/output.bam test-data/ref.fa.gz test-data/t_R1.fastq.gz test-data/t_R2.fastq.gz tool-data/bwameth_indexes.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r f7094efef903 bwameth.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwameth.xml Wed Sep 14 16:55:47 2016 -0400 |
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| @@ -0,0 +1,118 @@ +<tool id="bwameth" name="bwameth" version="0.2.0"> + <description>Fast and accurate aligner of BS-Seq reads.</description> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="0.2.0">bwameth</requirement> + </requirements> + <version_command>bwameth.py --version</version_command> + <command detect_errors="aggressive"> +<![CDATA[ + #if $referenceSource.source != "indexed": + mkdir index_dir && + ln -s '$referenceSource.reference' index_dir/genome.fa && + bwameth.py index index_dir/genome.fa && + #set index="index_dir/genome.fa" + #else + #set index=$referenceSource.index.fields.path + #end if + + bwameth.py + -t "\${GALAXY_SLOTS:-4}" + --reference "${index}" + + #if str($readGroup).strip() != "": + --read-group "${readGroup}" + #end if + + #if $single_or_paired.single_or_paired_opts == 'single': + $single_or_paired.input_singles + #elif $single_or_paired.single_or_paired_opts == 'paired': + $single_or_paired.input_mate1 $single_or_paired.input_mate2 + #else: + $single_or_paired.input_mate1.forward $single_or_paired.input_mate1.reverse + #end if + | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -o output.bam - +]]> + </command> + <inputs> + <conditional name="referenceSource"> + <param name="source" type="select" label="Select a genome reference from your history or a built-in index?"> + <option value="history" selected="True">Use one from the history</option> + <option value="indexed">Use a built-in index</option> + </param> + <when value="history"> + <param name="reference" type="data" format="fasta" metadata_name="dbkey" label="Select a genome" help="in FASTA format" /> + </when> + <when value="indexed"> + <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin"> + <options from_data_table="bwameth_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + </conditional> + + <conditional name="single_or_paired"> + <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + <option value="paired_collection">Paired-end Dataset Collection</option> + </param> + <when value="single"> + <param name="input_singles" type="data" format="fastqsanger" label="FASTQ" help="FASTQ file." /> + </when> + <when value="paired"> + <param name="input_mate1" type="data" format="fastqsanger" label="First read in pair" help="FASTQ file." /> + <param name="input_mate2" type="data" format="fastqsanger" label="Second read in pair" help="FASTQ file." /> + </when> + <when value="paired_collection"> + <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." /> + </when> + </conditional> + <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'"> + <sanitizer sanitize="False"/> + </param> + </inputs> + <outputs> + <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="referenceSource" value="history" /> + <param name="reference" value="ref.fa.gz" /> + <param name="single_or_paired_opts" value="paired" /> + <param name="input_mate1" value="t_R1.fastq.gz" /> + <param name="input_mate2" value="t_R2.fastq.gz" /> + <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> + </test> + <test> + <param name="referenceSource" value="history" /> + <param name="reference" value="ref.fa.gz" /> + <param name="single_or_paired_opts" value="paired_collection" /> + <param name="input_mate1"> + <collection type="paired"> + <element name="forward" value="t_R1.fastq.gz" /> + <element name="reverse" value="t_R2.fastq.gz" /> + </collection> + </param> + <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> + </test> + </tests> + <help> +<![CDATA[ + +**What it does** + +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> + <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}, + Title = {Fast and accurate alignment of long bisulfite-seq reads}, + Year = {2014}, + Eprint = {arXiv:1401.1129}, + }</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r f7094efef903 tool-data/bwameth_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bwameth_indexes.loc.sample Wed Sep 14 16:55:47 2016 -0400 |
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| @@ -0,0 +1,10 @@ +# This is a sample file distributed with Galaxy that is used to define a +# list of bwa-meth indices, using three columns tab separated: +# +# bwameth_index_id\tSome description text\t/path/to/genome.fasta +# +# An index can be created with the following command: +# +# bwameth.py index /some/path/genome.fa +# +# "/some/path/genome.fa" would then be the last column in the line |
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| diff -r 000000000000 -r f7094efef903 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Sep 14 16:55:47 2016 -0400 |
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| @@ -0,0 +1,6 @@ +<tables> + <table name="bwameth_indexes" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/bwameth_indexes.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r f7094efef903 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 14 16:55:47 2016 -0400 |
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| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bwameth" version="0.2.0"> + <repository changeset_revision="54d14a994f71" name="package_python_2_7_bwameth_0_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |