Mercurial > repos > drosofff > msp_sr_bowtie
changeset 6:b7173c0011f3 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 0d4bc357e7f0b13488806ebdab71090411d9b430
| author | drosofff |
|---|---|
| date | Mon, 10 Jul 2017 13:20:28 -0400 |
| parents | b2c1ffe6579a |
| children | |
| files | sRbowtie.xml |
| diffstat | 1 files changed, 12 insertions(+), 10 deletions(-) [+] |
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--- a/sRbowtie.xml Tue Jul 04 18:29:02 2017 -0400 +++ b/sRbowtie.xml Mon Jul 10 13:20:28 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.2"> +<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.3"> <description>for FASTA small reads</description> <requirements> <requirement type="package" version="1.1.2=py27_2">bowtie</requirement> @@ -6,9 +6,11 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ #if $refGenomeSource.genomeSource == "history": - bowtie-build -f $refGenomeSource.ownFile local_index && + bowtie-build -f $refGenomeSource.ownFile genome && + ln -s -f '$refGenomeSource.ownFile' genome.fa && + #set index_path = 'genome' #else: - ln -f -s $refGenomeSource.index.fields.path local_index && + #set index_path = $refGenomeSource.index.fields.path #end if #if $input.extension == "fasta": #set format = "-f" @@ -46,16 +48,16 @@ ## run the bowtie alignement #if $output_format == "tabular": - bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > $output + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $index_path $format '$input' > $output #elif $output_format == "sam": - bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output' + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' > '$output' #elif $output_format == "bam": - bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output #end if ##### | samtools view -uS ]]></command> <inputs> - <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" /> + <param format="fasta, fastq" help="Only with clipped, fasta or fastq read files" label="Input fasta or fastq file: reads clipped from their adapter" name="input" type="data" /> <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select"> <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option> <option value="unique">Match unique mappers on DNA reference index</option> @@ -181,7 +183,7 @@ However, this Bowtie wrapper tool only takes FASTQ files as inputs. -The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode) +The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis. ------ @@ -226,13 +228,13 @@ .. class:: warningmark -*The only accepted format for the script is a raw fasta list of reads, clipped from their adapter* +*Lists of reads, in fasta or fastq format, clipped from their adapter sequence* ----- **OUTPUTS** -If you choose tabular as the output format, you will obtain the matched reads in standard bowtie output format, having the following columns:: +If you choose tabular as the output format, you will obtain the matched reads in tabular bowtie output format, having the following columns:: Column Description -------- --------------------------------------------------------