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1 <tool id="rsem_prepare_reference" name="RSEM prepare reference" version="EBA2016-v1">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.2.28">rsem</requirement>
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5 <requirement type="package" version="1.1.2">bowtie</requirement>
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6 <requirement type="package" version="2.2.6">bowtie2</requirement>
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7 </requirements>
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8 <command>
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9 echo $reference_name " " | tee $reference_file &&
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10 mkdir $reference_file.files_path &&
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11 cd $reference_file.files_path &&
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12 rsem-prepare-reference
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13 #if $polya.polya_use == 'add':
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14 #if $polya.polya_length:
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15 --polyA-length $polya.polya_length
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16 #end if
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17 #elif $polya.polya_use == 'subset':
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18 --no-polyA-subset $polya.no_polya_subset
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19 #if $polya.polya_length:
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20 --polyA-length $polya.polya_length
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21 #end if
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22 #elif $polya.polya_use == 'none':
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23 --no-polyA
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24 #end if
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25 $ntog
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1
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26 $bowtie
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27 $bowtietwo
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28 #if $transcript_to_gene_map:
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29 --transcript-to-gene-map $transcript_to_gene_map
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30 #end if
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31 #if $reference.ref_type == 'transcripts':
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32 $reference.reference_fasta_file
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33 #else:
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34 #if $reference.gtf.extension == 'gtf':
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35 --gtf $reference.gtf
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36 #elif $reference.gtf.extension == 'gff3':
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37 --gff3 $reference.gtf
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38 #end if
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39 $reference.reference_fasta_file
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40 #end if
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41 $reference_name
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42 > ${reference_name}.log
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43 </command>
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44 <inputs>
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45 <conditional name="reference">
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46 <param name="ref_type" type="select" label="Reference transcript source">
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47 <option value="transcripts">transcript fasta</option>
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48 <option value="genomic">reference genome and gtf</option>
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49 </param>
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50 <when value="transcripts">
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51 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
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52 help="The files should contain the sequences of transcripts."/>
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53 </when>
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54 <when value="genomic">
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55 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
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56 help="The file should contain the sequence of an entire genome."/>
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57 <param name="gtf" type="data" format="gtf,gff3" label="gtf or gff3 file"
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58 help="extract transcript reference sequences using the gene annotations specified in this GTF or GFF3 file" />
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59 </when>
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60 </conditional>
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61 <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" >
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62 <help>
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63 Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character )
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64 The map can be obtained from the UCSC table browser
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65 group: Genes and Gene Prediction Tracks
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66 table: knownIsoforms
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67 Without a map:
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68 If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file.
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69 Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.
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70 </help>
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71 </param>
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72 <param name="reference_name" type="text" value="rsem_ref_name" label="reference name">
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73 <help>A one word name for this RSEM reference containing only letters, digits, and underscore characters</help>
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74 <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator>
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75 </param>
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76 <conditional name="polya">
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77 <param name="polya_use" type="select" label="PolyA ">
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78 <option value="add" selected="true">Add poly(A) tails to all transcripts</option>
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79 <option value="subset">Exclude poly(A) tails from selected transcripts</option>
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80 <option value="none">Do not add poly(A) tails to any transcripts</option>
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81 </param>
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82 <when value="add">
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83 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">
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84 <validator type="in_range" message="must be positive " min="1"/>
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85 </param>
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86 </when>
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87 <when value="subset">
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88 <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."/>
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89 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">
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90 <validator type="in_range" message="must be positive " min="1"/>
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91 </param>
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92 </when>
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93 <when value="none"/>
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94 </conditional>
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95 <param name="bowtie" type="boolean" truevalue="--bowtie" falsevalue="" checked="false" label="Use bowtie" />
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96 <param name="bowtietwo" type="boolean" truevalue="--bowtie2" falsevalue="" checked="false" label="Use bowtie2" />
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97 <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."/>
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98 </inputs>
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99 <stdio>
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100 <exit_code range="1:" level="fatal" description="Error Running RSEM" />
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101 </stdio>
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102 <outputs>
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103 <data format="rsem_ref" name="reference_file" label="RSEM ${reference_name} reference"/>
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104 </outputs>
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105 <tests>
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106 <test>
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107 <param name="ref_type" value="genomic"/>
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108 <param name="reference_fasta_file" value="ref.fasta" ftype="fasta"/>
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109 <param name="gtf" value="ref.gtf" ftype="gtf"/>
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110 <param name="reference_name" value="ref"/>
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111 <output name="rsem_ref">
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112 <assert_contents>
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113 <has_text text="ref.grp" />
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114 </assert_contents>
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115 </output>
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116 </test>
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117 </tests>
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118 <help>
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119
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120 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
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121
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122 NAME
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123 rsem-prepare-reference
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124
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125 SYNOPSIS
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126 rsem-prepare-reference [options] reference_fasta_file(s) reference_name
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127
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128 DESCRIPTION
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129 The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters.
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130 This program is used in conjunction with the 'rsem-calculate-expression' program.
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131
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132 INPUTS
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133 A fasta file of transcripts
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134 or
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135 A genome sequence fasta file and a GTF gene annotation file. (When using UCSC data, include the related knownIsoforms.txt)
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136
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137 </help>
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138 </tool>
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