Mercurial > repos > iuc > bwameth
changeset 5:29bdbc353f20 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth commit 823259bba9405d22dc2add24746057122c819ad3"
| author | iuc |
|---|---|
| date | Tue, 01 Oct 2019 17:53:32 -0400 |
| parents | 95219305823a |
| children | b4e6819b25ef |
| files | bwameth.xml |
| diffstat | 1 files changed, 72 insertions(+), 75 deletions(-) [+] |
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--- a/bwameth.xml Thu Nov 09 13:07:16 2017 -0500 +++ b/bwameth.xml Tue Oct 01 17:53:32 2019 -0400 @@ -1,86 +1,85 @@ -<tool id="bwameth" name="bwameth" version="0.2.0.4" profile="17.01"> +<tool id="bwameth" name="bwameth" version="@TOOL_VERSION@" profile="17.01"> <description>Fast and accurate aligner of BS-Seq reads.</description> + <macros> + <token name="@TOOL_VERSION@">0.2.2</token> + </macros> <requirements> - <requirement type="package" version="0.2.0">bwameth</requirement> - <requirement type="package" version="0.7.16">bwa</requirement> + <requirement type="package" version="@TOOL_VERSION@">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 + <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=$referenceSource.index.fields.path +#end if - ## Link in the files with a name that's appropriate - #if str($single_or_paired.single_or_paired_opts) == 'paired': - #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"): - #set read1 = "input_f.fastq.gz" - #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set read1 = "input_f.fastq.bz2" - #else: - #set read1 = "input_f.fastq" - #end if - ln -f -s '${single_or_paired.input_mate1}' ${read1} && +## Link in the files with a name that's appropriate +#if str($single_or_paired.single_or_paired_opts) == 'paired': + #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read1 = "input_f.fastq.gz" + #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read1 = "input_f.fastq.bz2" + #else: + #set read1 = "input_f.fastq" + #end if + ln -f -s '${single_or_paired.input_mate1}' ${read1} && - #if $single_or_paired.input_mate2.is_of_type("fastq.gz", "fastqsanger.gz"): - #set read2 = "input_r.fastq.gz" - #else if $single_or_paired.input_mate2.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set read2 = "input_r.fastq.bz2" - #else: - #set read2 = "input_r.fastq" - #end if - ln -f -s '${single_or_paired.input_mate2}' ${read2} && - #else if str($single_or_paired.single_or_paired_opts) == 'paired_collection': - #if $single_or_paired.input_mate1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): - #set read1 = "input_f.fastq.gz" - #else if $single_or_paired.input_mate1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set read1 = "input_f.fastq.bz2" - #else: - #set read1 = "input_f.fastq" - #end if - ln -s '${single_or_paired.input_mate1.forward}' ${read1} && + #if $single_or_paired.input_mate2.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read2 = "input_r.fastq.gz" + #else if $single_or_paired.input_mate2.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read2 = "input_r.fastq.bz2" + #else: + #set read2 = "input_r.fastq" + #end if + ln -f -s '${single_or_paired.input_mate2}' ${read2} && +#else if str($single_or_paired.single_or_paired_opts) == 'paired_collection': + #if $single_or_paired.input_mate1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read1 = "input_f.fastq.gz" + #else if $single_or_paired.input_mate1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read1 = "input_f.fastq.bz2" + #else: + #set read1 = "input_f.fastq" + #end if + ln -s '${single_or_paired.input_mate1.forward}' ${read1} && - #if $single_or_paired.input_mate1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): - #set read2 = "input_r.fastq.gz" - #else if $single_or_paired.input_mate1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set read2 = "input_r.fastq.bz2" - #else: - #set read2 = "input_r.fastq" - #end if - ln -s '${single_or_paired.input_mate1.reverse}' ${read2} && + #if $single_or_paired.input_mate1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read2 = "input_r.fastq.gz" + #else if $single_or_paired.input_mate1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read2 = "input_r.fastq.bz2" #else: - #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"): - #set read1 = "input_f.fastq.gz" - #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set read1 = "input_f.fastq.bz2" - #else: - #set read1 = "input_f.fastq" - #end if - ln -f -s '${single_or_paired.input_singles}' ${read1} && + #set read2 = "input_r.fastq" #end if - + ln -s '${single_or_paired.input_mate1.reverse}' ${read2} && +#else: + #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"): + #set read1 = "input_f.fastq.gz" + #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set read1 = "input_f.fastq.bz2" + #else: + #set read1 = "input_f.fastq" + #end if + ln -f -s '${single_or_paired.input_singles}' ${read1} && +#end if - bwameth.py - -t "\${GALAXY_SLOTS:-4}" - --reference "${index}" +bwameth.py +-t "\${GALAXY_SLOTS:-4}" +--reference '${index}' - #if str($readGroup).strip() != "": - --read-group "${readGroup}" - #end if +#if str($readGroup).strip(): + --read-group '${readGroup}' +#end if - #if $single_or_paired.single_or_paired_opts == 'single': - $read1 - #else: - $read1 $read2 - #end if - | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam - -]]> - </command> +#if $single_or_paired.single_or_paired_opts == 'single': + $read1 +#else: + $read1 $read2 +#end if +| samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" -O bam -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?"> @@ -146,14 +145,12 @@ <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> </test> </tests> - <help> -<![CDATA[ + <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> + ]]></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},