Mercurial > repos > jjohnson > rsem
view rsem_prepare_reference.xml @ 5:14267d364365 default tip
Update for dataset files_path - use model from BB pull request 532
author | Jim Johnson <jj@umn.edu> |
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date | Thu, 04 Feb 2016 06:50:26 -0600 |
parents | 30a8343fb0e7 |
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<tool id="rsem_prepare_reference" name="RSEM prepare reference" version="1.1.17"> <description></description> <requirements> <requirement type="package" version="1.1.17">rsem</requirement> <requirement type="package" version="1.0.0">bowtie</requirement> </requirements> <command> echo $reference_name " " | tee $reference_file && mkdir $reference_file.files_path && cd $reference_file.files_path && rsem-prepare-reference #if $polya.polya_use == 'add': #if $polya.polya_length: --polyA-length $polya.polya_length #end if #elif $polya.polya_use == 'subset': --no-polyA-subset $polya.no_polya_subset #if $polya.polya_length: --polyA-length $polya.polya_length #end if #elif $polya.polya_use == 'none': --no-polyA #end if $ntog #if $transcript_to_gene_map: --transcript-to-gene-map $transcript_to_gene_map #end if #if $reference.ref_type == 'transcripts': $reference.reference_fasta_file #else: --gtf $reference.gtf $reference.reference_fasta_file #end if $reference_name > ${reference_name}.log </command> <inputs> <conditional name="reference"> <param name="ref_type" type="select" label="Reference transcript source"> <option value="transcripts">transcript fasta</option> <option value="genomic">reference genome and gtf</option> </param> <when value="transcripts"> <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" help="The files should contain the sequences of transcripts."/> </when> <when value="genomic"> <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" help="The file should contain the sequence of an entire genome."/> <param name="gtf" type="data" format="gtf" label="gtf" help="extract transcript reference sequences using the gene annotations specified in this GTF" /> </when> </conditional> <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" > <help> Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character ) The map can be obtained from the UCSC table browser group: Genes and Gene Prediction Tracks table: knownIsoforms Without a map: If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file. Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene. </help> </param> <param name="reference_name" type="text" value="rsem_ref_name" label="reference name"> <help>A one word name for this RSEM reference containing only letters, digits, and underscore characters</help> <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator> </param> <conditional name="polya"> <param name="polya_use" type="select" label="PolyA "> <option value="add" selected="true">Add poly(A) tails to all transcripts</option> <option value="subset">Exclude poly(A) tails from selected transcripts</option> <option value="none">Do not add poly(A) tails to any transcripts</option> </param> <when value="add"> <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)"> <validator type="in_range" message="must be positive " min="1"/> </param> </when> <when value="subset"> <param name="no_polya_subset" type="data" format="tabular" optional="true" label="List of transcript IDs (one per line) that should should not have polyA tails added."/> <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)"> <validator type="in_range" message="must be positive " min="1"/> </param> </when> <when value="none"/> </conditional> <param name="ntog" type="boolean" truevalue="--no-ntog" falsevalue="" checked="false" label="Disable the conversion of 'N' characters to 'G' characters in the reference sequences" help="Bowite uses the automatic N to G conversion to to align against all positions in the reference."/> </inputs> <stdio> <exit_code range="1:" level="fatal" description="Error Running RSEM" /> </stdio> <outputs> <data format="rsem_ref" name="reference_file" label="RSEM ${reference_name} reference"/> </outputs> <tests> <test> <param name="ref_type" value="genomic"/> <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> <param name="gtf" value="ref.gtf" ftype="gtf"/> <param name="reference_name" value="ref"/> <output name="rsem_ref"> <assert_contents> <has_text text="ref.grp" /> </assert_contents> </output> </test> </tests> <help> RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/ NAME rsem-prepare-reference SYNOPSIS rsem-prepare-reference [options] reference_fasta_file(s) reference_name DESCRIPTION The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters. This program is used in conjunction with the 'rsem-calculate-expression' program. INPUTS A fasta file of transcripts or A genome sequence fasta file and a GTF gene annotation file. (When using UCSC data, include the related knownIsoforms.txt) </help> </tool>