Mercurial > repos > drosofff > srbowtie_cascade
changeset 0:6f25e1dac784 draft
Uploaded
| author | drosofff |
|---|---|
| date | Sun, 22 Jun 2014 13:08:56 -0400 |
| parents | |
| children | 4c7013211739 |
| files | sRbowtieCascade.xml |
| diffstat | 1 files changed, 142 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sRbowtieCascade.xml Sun Jun 22 13:08:56 2014 -0400 @@ -0,0 +1,142 @@ +<tool id="sRbowtie_cascade" name="Annotate smRNA datasets" version="0.9.0"> + <description>Using iterative sRbowtie Alignments</description> + <requirements> + <requirement type='package'>bowtie</requirement> + </requirements> + <parallelism method="basic"></parallelism> + <command interpreter="python"> sRbowtieCascade.py --output $output + --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie + --mismatch $mismatches + --input + #for $i in $input: + $i + #end for + --label + #for $i in $input: + "$i.name" + #end for + --index + #if $refGenomeSource1.genomeSource == "history": + $refGenomeSource1.ownFile + #else: + $refGenomeSource1.index.fields.path + #end if + #for $i in $AdditionalQueries: + #if $i.refGenomeSource.genomeSource == "history": + $i.refGenomeSource.ownFile + #else: + $i.refGenomeSource.index.fields.path + #end if + #end for + --indexing-flags + $refGenomeSource1.genomeSource + #for $i in $AdditionalQueries: + $i.refGenomeSource.genomeSource + #end for + --indexName + #if $refGenomeSource1.genomeSource == "history": + "$refGenomeSource1.ownFile.name" + #else: + "$refGenomeSource1.index.fields.name" + #end if + #for $i in $AdditionalQueries: + #if $i.refGenomeSource.genomeSource == "history": + "$i.refGenomeSource.ownFile.name" + #else: + "$i.refGenomeSource.index.fields.name" + #end if + #end for + </command> + <inputs> + <param name="input" type="data" format="fasta" label="Input fasta file: reads clipped from their adapter" help="Only with clipped, raw fasta files" multiple="true"/> + <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments"> + <option value="0">0</option> + <option value="1" selected="true">1</option> + <option value="2">2</option> + <option value="3">3</option> + </param> +<!-- First bowtie index selection --> + <conditional name="refGenomeSource1"> + <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact GED team"> + <options from_data_table="bowtie_indexes"/> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" /> + </when> + </conditional> +<!-- End of first bowtie index selection --> +<!-- other bowtie index selections --> + <repeat name="AdditionalQueries" title="Additional Alignment Step"> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact GED team"> + <options from_data_table="bowtie_indexes"/> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" /> + </when> + </conditional> + </repeat> +<!-- End of other bowtie index selections --> + </inputs> + <outputs> + <data format="tabular" name="output" label="Cascade Annotation Analysis"/> + </outputs> + + <test> + </test> + + <help> + +**Intro** + +Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. +A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution. +However, this Bowtie wrapper tool only takes FASTQ files as inputs. + +Here The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode, with -k 1) + +.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml + + +------ + +**What it does** + +.. class:: infomark + +This script uses the sRbowtie wrapper to iteratively match reads on a reference indexes. + +Reads are Matched on DNA references as fast as possible, without taking care of mapping issues + +*-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8* + +unaligned reads at step N are used input for sRbowtie at step N+1 + +----- + +**Input formats** + +.. class:: warningmark + +*The only accepted format for the script is a raw fasta list of reads, clipped from their adapter* + +----- + +**OUTPUTS** + +**Annotation table** + + </help> +</tool>