Mercurial > repos > jjohnson > rsem
annotate rsem_prepare_reference.xml @ 3:59459de65740
mv RSEM datatypes to separate repository, remove samtools dependency
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 10 Mar 2014 07:19:56 -0500 |
| parents | ca988deacfd1 |
| children | 30a8343fb0e7 |
| 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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59459de65740
mv RSEM datatypes to separate repository, remove samtools dependency
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
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8 echo $reference_name " " | tee $reference_file && |
| 0 | 9 mkdir $reference_file.extra_files_path && |
| 10 cd $reference_file.extra_files_path && | |
| 11 rsem-prepare-reference | |
| 12 #if $polya.polya_use == 'add': | |
| 13 #if $polya.polya_length: | |
| 14 --polyA-length $polya.polya_length | |
| 15 #end if | |
| 16 #elif $polya.polya_use == 'subset': | |
| 17 --no-polyA-subset $polya.no_polya_subset | |
| 18 #if $polya.polya_length: | |
| 19 --polyA-length $polya.polya_length | |
| 20 #end if | |
| 21 #elif $polya.polya_use == 'none': | |
| 22 --no-polyA | |
| 23 #end if | |
| 24 $ntog | |
| 25 #if $transcript_to_gene_map: | |
| 26 --transcript-to-gene-map $transcript_to_gene_map | |
| 27 #end if | |
| 28 #if $reference.ref_type == 'transcripts': | |
| 29 $reference.reference_fasta_file | |
| 30 #else: | |
| 31 --gtf $reference.gtf | |
| 32 $reference.reference_fasta_file | |
| 33 #end if | |
| 34 $reference_name | |
|
3
59459de65740
mv RSEM datatypes to separate repository, remove samtools dependency
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
35 > ${reference_name}.log |
| 0 | 36 </command> |
| 37 <inputs> | |
| 38 <conditional name="reference"> | |
| 39 <param name="ref_type" type="select" label="Reference transcript source"> | |
| 40 <option value="transcripts">transcript fasta</option> | |
| 41 <option value="genomic">reference genome and gtf</option> | |
| 42 </param> | |
| 43 <when value="transcripts"> | |
| 44 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" | |
| 45 help="The files should contain the sequences of transcripts."/> | |
| 46 </when> | |
| 47 <when value="genomic"> | |
| 48 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file" | |
| 49 help="The file should contain the sequence of an entire genome."/> | |
| 50 <param name="gtf" type="data" format="gtf" 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="rsem_ref_name" label="reference name"> | |
|
3
59459de65740
mv RSEM datatypes to separate repository, remove samtools dependency
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
66 <help>A one word name for this RSEM reference containing only letters, digits, and underscore characters</help> |
| 0 | 67 <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator> |
| 68 </param> | |
| 69 <conditional name="polya"> | |
| 70 <param name="polya_use" type="select" label="PolyA "> | |
| 71 <option value="add" selected="true">Add poly(A) tails to all transcripts</option> | |
| 72 <option value="subset">Exclude poly(A) tails from selected transcripts</option> | |
| 73 <option value="none">Do not add poly(A) tails to any transcripts</option> | |
| 74 </param> | |
| 75 <when value="add"> | |
| 76 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)"> | |
| 77 <validator type="in_range" message="must be positive " min="1"/> | |
| 78 </param> | |
| 79 </when> | |
| 80 <when value="subset"> | |
| 81 <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."/> | |
| 82 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)"> | |
| 83 <validator type="in_range" message="must be positive " min="1"/> | |
| 84 </param> | |
| 85 </when> | |
| 86 <when value="none"/> | |
| 87 </conditional> | |
| 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 <tests> | |
| 97 <test> | |
| 98 <param name="ref_type" value="genomic"/> | |
| 99 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/> | |
| 100 <param name="gtf" value="ref.gtf" ftype="gtf"/> | |
| 101 <param name="reference_name" value="ref"/> | |
| 102 <output name="rsem_ref"> | |
| 103 <assert_contents> | |
| 104 <has_text text="ref.grp" /> | |
| 105 </assert_contents> | |
| 106 </output> | |
| 107 </test> | |
| 108 </tests> | |
| 109 <help> | |
| 110 | |
| 111 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/ | |
| 112 | |
| 113 NAME | |
| 114 rsem-prepare-reference | |
| 115 | |
| 116 SYNOPSIS | |
| 117 rsem-prepare-reference [options] reference_fasta_file(s) reference_name | |
| 118 | |
| 119 DESCRIPTION | |
| 120 The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters. | |
| 121 This program is used in conjunction with the 'rsem-calculate-expression' program. | |
| 122 | |
| 123 INPUTS | |
| 124 A fasta file of transcripts | |
| 125 or | |
| 126 A genome sequence fasta file and a GTF gene annotation file. (When using UCSC data, include the related knownIsoforms.txt) | |
| 127 | |
| 128 </help> | |
| 129 </tool> |