Mercurial > repos > jjohnson > rsem

comparison rsem_prepare_reference.xml @ 0:64d45f959303

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jjohnson
date Mon, 11 Nov 2013 13:54:43 -0500
parents
children 1ff2fc8da328
comparison
equal deleted inserted replaced
-1:000000000000 0:64d45f959303
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>
8 rsem-prepare-reference
9 #if $polya.polya_use == 'add':
10 #if $polya.polya_length:
11 --polyA-length $polya.polya_length
12 #end if
13 #elif $polya.polya_use == 'subset':
14 --no-polyA-subset $polya.no_polya_subset
15 #if $polya.polya_length:
16 --polyA-length $polya.polya_length
17 #end if
18 #elif $polya.polya_use == 'none':
19 --no-polyA
20 #end if
21 $ntog
22 #if $transcript_to_gene_map:
23 --transcript-to-gene-map $transcript_to_gene_map
24 #end if
25 #if $reference.ref_type == 'transcripts':
26 $reference.reference_fasta_file
27 #else:
28 --gtf $reference.gtf
29 $reference.reference_fasta_file
30 #end if
31 $reference_name
32 </command>
33
34 <inputs>
35 <conditional name="reference">
36 <param name="ref_type" type="select" label="">
37 <option value="transcripts">transcript fasta</option>
38 <option value="genomic">reference genome and gtf</option>
39 </param>
40 <when value="transcripts">
41 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
42 help="The files should contain the sequences of transcripts."/>
43
44 </when>
45 <when value="genomic">
46 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
47 help="The files should contain either the sequences of an entire genome."/>
48 <param name="gtf" type="data" format="gtf" optional="true" label="gtf"
49 help="extract transcript reference sequences using the gene annotations specified in this GTF" />
50 </when>
51 </conditional>
52 <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" >
53 <help>
54 Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character )
55 The map can be obtained from the UCSC table browser
56 group: Genes and Gene Prediction Tracks
57 table: knownIsoforms
58 Without a map:
59 If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file.
60 Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.
61 </help>
62 </param>
63 <param name="reference_name" type="text" value="" label="reference name">
64 </param>
65
66 <conditional name="polya">
67 <param name="polya_use" type="select" label="PolyA ">
68 <option value="add" selected="true">Add poly(A) tails to all transcripts</option>
69 <option value="subset">Exclude poly(A) tails from selected transcripts</option>
70 <option value="none">Do not add poly(A) tails to any transcripts</option>
71 </param>
72 <when value="add">
73 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">
74 <validator type="in_range" message="must be positive " min="1"/>
75 </param>
76 </when>
77 <when value="subset">
78 <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."/>
79 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">
80 <validator type="in_range" message="must be positive " min="1"/>
81 </param>
82 </when>
83 <when value="none"/>
84 </conditional>
85
86 <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."/>
87 </inputs>
88 <stdio>
89 <exit_code range="1:" level="fatal" description="Error Running RSEM" />
90 </stdio>
91 <outputs>
92 <data format="rsem_ref" name="reference_file" label="RSEM ${reference_name} reference"/>
93 </outputs>
94 <help>
95
96
97 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
98
99 NAME
100 rsem-prepare-reference
101
102 SYNOPSIS
103 rsem-prepare-reference [options] reference_fasta_file(s) reference_name
104
105 DESCRIPTION
106 The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters.
107 This program is used in conjunction with the 'rsem-calculate-expression' program.
108
109 INPUTS
110
111
112
113 </help>
114 </tool>