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annotate trinity.xml @ 18:d3b1249af60c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
author iuc
date Tue, 19 Dec 2017 04:21:46 -0500
parents 199aa6821ca5
children cee61b3fcf78
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d3b1249af60c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit aee00b3755588862ab34c199c28578706c004a34
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1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.2">
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2 <description>de novo assembly of RNA-Seq data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="aggressive"><![CDATA[
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8 #if $additional_params.guided.is_guided == "yes":
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9 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
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10 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
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11 #end if
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12 Trinity --no_version_check
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14 ## Inputs.
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15 #if $inputs.paired_or_single == "paired":
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17 --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) }
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19 --right ${ ','.join(['"%s"' % x for x in $inputs.right_input]) }
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21 #if $inputs.left_input[0].is_of_type('fasta'):
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22 --seqType fa
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23 #else:
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24 --seqType fq
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25 #end if
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27 @COMMAND_PAIRED_STRAND_JACCARD@
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29 #elif $inputs.paired_or_single == "paired_collection"
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30 --left ${ ','.join(['"%s"' % x.forward for x in $inputs.pair_input]) }
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32 --right ${ ','.join(['"%s"' % x.reverse for x in $inputs.pair_input]) }
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34 #if $inputs.pair_input[0].forward.is_of_type('fasta'):
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35 --seqType fa
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36 #else:
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37 --seqType fq
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38 #end if
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39
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40 @COMMAND_PAIRED_STRAND_JACCARD@
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42 #else:
3
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43 --single ${ ','.join(['"%s"' % x for x in $inputs.input]) }
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45 #if $inputs.input[0].is_of_type('fasta'):
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46 --seqType fa
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47 #else:
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48 --seqType fq
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49 #end if
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0
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51 #if $inputs.strand.is_strand_specific:
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52 --SS_lib_type $inputs.strand.library_type
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53 #end if
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54 #end if
3
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0
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56 $norm
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58 ## Additional parameters.
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59 #if $additional_params.min_contig_length:
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60 --min_contig_length $additional_params.min_contig_length
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61 #end if
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62 #if $additional_params.long_reads:
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63 --long_reads $additional_params.long_reads
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64 #end if
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65 #if $additional_params.guided.is_guided == "yes":
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66 --genome_guided_bam 'localbam.bam'
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67
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68 #if $additional_params.guided.genome_guided_min_coverage:
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69 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
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70 #end if
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71
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72 #if $additional_params.guided.genome_guided_min_reads_per_partition:
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73 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
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74 #end if
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75
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76 #if $additional_params.guided.genome_guided_max_intron:
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77 --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron
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78 #end if
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79
0
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80 #end if
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81
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82 #if $additional_params.min_kmer_cov:
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83 --min_kmer_cov $additional_params.min_kmer_cov
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84 #end if
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85
0
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86 ## CPU and butterfly options.
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87 --CPU \${GALAXY_SLOTS:-4} --max_memory \${TRINITY_MAX_MEMORY:-1G} --bflyHeapSpaceMax \${TRINITY_MAX_MEMORY:-1G} --bfly_opts '-V 10 --stderr'
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88
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89 ## > $trinity_log 2>&1
0
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90 ]]></command>
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91 <inputs>
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92 <conditional name="inputs">
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93 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
17
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94 <option value="single">Single-end</option>
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95 <option value="paired" selected="true">Paired-end</option>
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96 <option value="paired_collection">Paired-end collection</option>
0
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97 </param>
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98 <when value="single">
17
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99 <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/>
0
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100 <conditional name="strand">
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101 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
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102 <when value="false">
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103 </when>
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104 <when value="true">
10
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105 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
0
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106 <option value="F">F</option>
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107 <option value="R">R</option>
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108 </param>
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109 </when>
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110 </conditional>
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111 </when>
17
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112 <when value="paired">
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113 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" />
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114 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" />
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115 <expand macro="input_paired_strand_jaccard" />
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116 </when>
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117 <when value="paired_collection">
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118 <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/>
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119 <expand macro="input_paired_strand_jaccard" />
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120 </when>
0
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121 </conditional>
3
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122
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123 <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
0
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124
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125 <section name="additional_params" title="Additional Options" expanded="False">
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126 <param name="min_contig_length" argument="--min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
3
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127
0
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128 <conditional name="guided">
1
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129 <param name="is_guided" type="select" label="Use the genome guided mode?" help="If you already mapped the reads to the genome, Trinity can use this information">
0
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130 <option value="no">No</option>
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131 <option value="yes">Yes</option>
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132 </param>
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133 <when value="no">
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134 </when>
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135 <when value="yes">
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136 <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
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137 <param name="genome_guided_max_intron" argument="--genome_guided_max_intron" type="integer" value="" min="1" label="Maximum allowed intron length (also maximum fragment span on genome)"/>
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138 <param name="genome_guided_min_coverage" argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
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139 <param name="genome_guided_min_reads_per_partition" argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
0
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140 </when>
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141 </conditional>
3
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142
17
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143 <param name="long_reads" argument="--long_reads" type="data" format="fasta" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
3
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144
10
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145 <param name="min_kmer_cov" argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
0
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146 </section>
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147 </inputs>
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148 <outputs>
17
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149 <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
0
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150 </outputs>
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151 <tests>
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152 <test>
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153 <param name="paired_or_single" value="paired"/>
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154 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
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155 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
0
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156 <param name="is_strand_specific" value="true"/>
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157 <param name="norm" value="false"/>
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158 <param name="library_type" value="RF"/>
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159 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
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160 </test>
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161 <test>
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162 <param name="paired_or_single" value="paired"/>
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163 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
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164 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
0
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165 <param name="is_strand_specific" value="true"/>
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166 <param name="norm" value="true"/>
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167 <param name="library_type" value="RF"/>
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168 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
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169 </test>
17
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170 <test>
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171 <param name="paired_or_single" value="paired_collection"/>
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172 <param name="pair_input">
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173 <collection type="list:paired">
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174 <element name="pair1">
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175 <collection type="paired">
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176 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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177 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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178 </collection>
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179 </element>
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180 <element name="pair2">
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181 <collection type="paired">
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182 <element name="forward" value="reads.left.fq" ftype="fastqsanger" />
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183 <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/>
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184 </collection>
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185 </element>
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186 </collection>
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187 </param>
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188 <param name="is_strand_specific" value="true"/>
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189 <param name="norm" value="true"/>
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190 <param name="library_type" value="RF"/>
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191 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
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192 </test>
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193 </tests>
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194 <help>
17
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195 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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196
17
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197 .. _Trinity: http://trinityrnaseq.github.io
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198 </help>
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199
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200 <expand macro="citation" />
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201 </tool>