Mercurial > repos > drosofff > msp_sr_bowtie_cascade
diff sRbowtieCascade.xml @ 0:0528fced93a9 draft default tip
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
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| date | Wed, 27 May 2015 17:31:35 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sRbowtieCascade.xml Wed May 27 17:31:35 2015 -0400 @@ -0,0 +1,151 @@ +<tool id="sRbowtie_cascade" name="Annotate smRNA datasets" version="1.0.1"> + <description>Using iterative sRbowtie Alignments</description> + <requirements> + <requirement type="package" version="0.12.7">bowtie</requirement> + </requirements> + <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 instance administrator"> + <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 instance administrator"> + <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> + + + <tests> + <test> + <param name="input" value ="sample1.fa,sample2.fa,sample3.fa" ftype="fasta" /> + <param name="genomeSource" value="history" /> + <param name="ownFile" value ="dmel-2L-r6.04.fasta" ftype="fasta" /> + <param name="AdditionalQueries_0|refGenomeSource|genomeSource" value="history"/> + <param name="AdditionalQueries_0|refGenomeSource|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> + <param name="AdditionalQueries_1|refGenomeSource|genomeSource" value="history"/> + <param name="AdditionalQueries_1|refGenomeSource|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> + <output name="output" ftype="tabular" file="Cascade_Annotation_Analysis.tab" /> + </test> + </tests> + <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 as 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>