Mercurial > repos > jjohnson > rsem
annotate rsem_prepare_reference.xml @ 1:1ff2fc8da328
Updates to rsem_calculate_expression.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 05 Dec 2013 10:54:28 -0600 |
| parents | 64d45f959303 |
| children | f6b8155ab12a |
| rev | line source |
|---|---|
| 0 | 1 <tool id="rsem_prepare_reference" name="RSEM prepare reference" version="1.1.17"> |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.1.17">rsem</requirement> | |
| 5 <requirement type="package" version="1.0.0">bowtie</requirement> | |
| 6 </requirements> | |
| 7 <command> | |
|
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1ff2fc8da328
Updates to rsem_calculate_expression.xml
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
8 mkdir $reference_file.extra_files_path && |
|
1ff2fc8da328
Updates to rsem_calculate_expression.xml
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
9 cd $reference_file.extra_files_path && |
| 0 | 10 rsem-prepare-reference |
| 11 #if $polya.polya_use == 'add': | |
| 12 #if $polya.polya_length: | |
| 13 --polyA-length $polya.polya_length | |
| 14 #end if | |
| 15 #elif $polya.polya_use == 'subset': | |
| 16 --no-polyA-subset $polya.no_polya_subset | |
| 17 #if $polya.polya_length: | |
| 18 --polyA-length $polya.polya_length | |
| 19 #end if | |
| 20 #elif $polya.polya_use == 'none': | |
| 21 --no-polyA | |
| 22 #end if | |
| 23 $ntog | |
| 24 #if $transcript_to_gene_map: | |
| 25 --transcript-to-gene-map $transcript_to_gene_map | |
| 26 #end if | |
| 27 #if $reference.ref_type == 'transcripts': | |
| 28 $reference.reference_fasta_file | |
| 29 #else: | |
| 30 --gtf $reference.gtf | |
| 31 $reference.reference_fasta_file | |
| 32 #end if | |
| 33 $reference_name | |
| 34 </command> | |
| 35 | |
| 36 <inputs> | |
| 37 <conditional name="reference"> | |
| 38 <param name="ref_type" type="select" label=""> | |
| 39 <option value="transcripts">transcript fasta</option> | |
| 40 <option value="genomic">reference genome and gtf</option> | |
| 41 </param> | |
| 42 <when value="transcripts"> | |
| 43 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" | |
| 44 help="The files should contain the sequences of transcripts."/> | |
| 45 | |
| 46 </when> | |
| 47 <when value="genomic"> | |
| 48 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" | |
| 49 help="The files should contain either the sequences of an entire genome."/> | |
| 50 <param name="gtf" type="data" format="gtf" optional="true" label="gtf" | |
| 51 help="extract transcript reference sequences using the gene annotations specified in this GTF" /> | |
| 52 </when> | |
| 53 </conditional> | |
| 54 <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" > | |
| 55 <help> | |
| 56 Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character ) | |
| 57 The map can be obtained from the UCSC table browser | |
| 58 group: Genes and Gene Prediction Tracks | |
| 59 table: knownIsoforms | |
| 60 Without a map: | |
| 61 If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file. | |
| 62 Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene. | |
| 63 </help> | |
| 64 </param> | |
| 65 <param name="reference_name" type="text" value="" label="reference name"> | |
| 66 </param> | |
| 67 | |
| 68 <conditional name="polya"> | |
| 69 <param name="polya_use" type="select" label="PolyA "> | |
| 70 <option value="add" selected="true">Add poly(A) tails to all transcripts</option> | |
| 71 <option value="subset">Exclude poly(A) tails from selected transcripts</option> | |
| 72 <option value="none">Do not add poly(A) tails to any transcripts</option> | |
| 73 </param> | |
| 74 <when value="add"> | |
| 75 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)"> | |
| 76 <validator type="in_range" message="must be positive " min="1"/> | |
| 77 </param> | |
| 78 </when> | |
| 79 <when value="subset"> | |
| 80 <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."/> | |
| 81 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)"> | |
| 82 <validator type="in_range" message="must be positive " min="1"/> | |
| 83 </param> | |
| 84 </when> | |
| 85 <when value="none"/> | |
| 86 </conditional> | |
| 87 | |
| 88 <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."/> | |
| 89 </inputs> | |
| 90 <stdio> | |
| 91 <exit_code range="1:" level="fatal" description="Error Running RSEM" /> | |
| 92 </stdio> | |
| 93 <outputs> | |
| 94 <data format="rsem_ref" name="reference_file" label="RSEM ${reference_name} reference"/> | |
| 95 </outputs> | |
| 96 <help> | |
| 97 | |
| 98 | |
| 99 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/ | |
| 100 | |
| 101 NAME | |
| 102 rsem-prepare-reference | |
| 103 | |
| 104 SYNOPSIS | |
| 105 rsem-prepare-reference [options] reference_fasta_file(s) reference_name | |
| 106 | |
| 107 DESCRIPTION | |
| 108 The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters. | |
| 109 This program is used in conjunction with the 'rsem-calculate-expression' program. | |
| 110 | |
| 111 INPUTS | |
| 112 | |
| 113 | |
| 114 | |
| 115 </help> | |
| 116 </tool> |