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author | biotechcoder |
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date | Fri, 01 May 2015 05:41:51 -0400 |
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<tool id="riboseqr_prepare_input" name="Prepare riboSeqR input" version="0.4.0"> <description> (Step 1) Prepare alignment file (SAM format, Ribo-Seq or RNA-Seq alignments) for riboSeqR analysis. </description> <requirements> <requirement type="R-module">riboSeqR</requirement> </requirements> <command interpreter="python">riboseqr/prepare.py #set $files_ribo = [] #set $files_rna = [] #set $replicates = [] #for $i, $s in enumerate($rnaseq.datasets) #silent $replicates.append($s.replicate_name.value) #silent $files_ribo.append($s.ribo_files.file_name) #try: #silent $s.rna_files #except: #pass #else: #silent $files_rna.append($s.rna_files.file_name) #end try #end for #set $ribofiles = ", ".join($files_ribo) #set $rnafiles = ", ".join($files_rna) #set $replicate_names = ", ".join($replicates) --ribo_files "$ribofiles" --rna_files "$rnafiles" --replicate_names "$replicate_names" --seqnames "$seqnames" --rdata_save "$rdata_save" --sam_format --html_file "$html_file" --output_path "$html_file.files_path" </command> <inputs> <conditional name="rnaseq"> <param name="have-rnaseq" type="boolean" truevalue="checked" falsevalue="unchecked" label="Have RNA-Seq data?"/> <when value="checked"> <repeat name="datasets" title="Ribo and RNA-Seq alignment" default="1"> <param type="text" name="replicate_name" size="20" label="Provide a common name for each replicate group" value=""/> <param format="sam" name="ribo_files" type="data" label="Ribo-Seq alignment file (SAM)" multiple="false"/> <param format="sam" name="rna_files" type="data" label="RNA-Seq alignment file (SAM)" multiple="false"/> </repeat> </when> <when value="unchecked"> <repeat name="datasets" title="Ribo-Seq alignment" default="1"> <param type="text" name="replicate_name" size="20" label="Provide a common name for each replicate group" value=""/> <param format="sam" name="ribo_files" type="data" label="Ribo-Seq alignment file (SAM)" multiple="false"> </param> </repeat> </when> </conditional> <param name="seqnames" type="text" area="True" label="Transcript (seqname) names to be read" size="3x60" help="[Optional] - only the mapped footprints for these transcripts will be used in further riboSeqR analysis. Multiple transcript names should be separated by commas. There should be no quotes around transcript names."> <sanitizer> <valid> <add value="|"/> </valid> </sanitizer> </param> </inputs> <outputs> <data format="rda" name="rdata_save" label="Prepare riboSeqR input (R data file)"/> <data format="html" name="html_file" label="Prepare riboSeqR input (HTML report)"/> </outputs> <tests> <test> <param name="ribo_files" value="12hRPF.sam" /> <output name="html_file" file="Prepare_riboSeqR_input_(HTML_report).html"> <extra_files type="file" name="RiboSeq file 1" value="RiboSeq file 1"/> </output> </test> </tests> <help> About ----- This tool can be used to prepare input data for riboSeqR from SAM format alignments of Ribo or RNA-Seq data to a reference transcriptome. You can do this alignment manually using bowtie or the "Transcriptome Mapping" -> "Align to transcriptome using Bowtie" tool on RiboGalaxy_ The required input format for riboSeqR_ is mentioned in the **"Getting Data"** section of the documentation_. riboSeqR version: **1.0.4**. How to use? ----------- Inputs ...... Select SAM format Ribo-Seq alignment files in the input section. If you have RNA-Seq data, these can be included if the **"Have RNA-Seq data"** option is checked. Outputs ....... The following files will be generated on completion: #. Prepare riboSeqR input (HTML report) - A HTML file with links to all other output files. * Generated riboSeqR format input files of RiboSeq and RNASeq data(if provided). These files are plain text and lines have the following information - strand, transcript name, alignment position, sequence. Please note the alignments are made **0-indexed**. * R script used in this session. #. Prepare riboSeqR input (R data file) - used as input for the next step - *Triplet Periodicity*. How are the SAM alignments processed? ..................................... #. Lines starting with ``@`` are ignored. #. Lines having a ``FLAG=0`` are considered as successful alignments. These are considered for the next step. #. Alignment start is located on ``column 4``. These are decremented by 1 as SAM alignments are 1-indexed. #. riboSeqR input file is written with the strand (``+``), transcript name, alignment start and the aligned sequence. riboSeqR functions used ....................... readRibodata. For detailed description of the functions and the options used, please consult the riboSeqR documentation. Links ..... * `Bioconductor package information on riboSeqR`__ * riboSeqR - `Reference manual`_ * riboSeqR - `Introduction and workflow example`_ .. _RiboGalaxy: http://ribogalaxy.ucc.ie .. _riboSeqR: http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html __ riboSeqR_ .. _manual: http://bioconductor.org/packages/3.0/bioc/manuals/riboSeqR/man/riboSeqR.pdf .. _`Reference manual`: manual_ .. _documentation: http://bioconductor.org/packages/3.0/bioc/vignettes/riboSeqR/inst/doc/riboSeqR.pdf .. _`Introduction and workflow example`: documentation_ </help> </tool>