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annotate trinity.xml @ 1:0067c78f49dc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1abd7a1cbd25b687267df2ebc4dfba5894797a64
author iuc
date Wed, 09 Dec 2015 07:19:52 -0500
parents 606b7748965d
children de0af39266ef
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0067c78f49dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1abd7a1cbd25b687267df2ebc4dfba5894797a64
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1 <tool id="trinity" name="Trinity" version="2.0.6.1">
0
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2 <description>de novo assembly of RNA-Seq data</description>
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3 <requirements>
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4 <requirement type="package" version="2.0.6">trinity</requirement>
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5 <requirement type="package" version="1.1.2">bowtie</requirement>
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6 <requirement type="package" version="1.2">samtools</requirement>
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7 <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement>
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8 </requirements>
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9 <command><![CDATA[
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10 Trinity
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11
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12 ## Inputs.
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13 #if $inputs.paired_or_single == "paired":
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14 --left $inputs.left_input --right $inputs.right_input
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16 #if $inputs.left_input.is_of_type('fasta'):
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17 --seqType fa
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18 #else:
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19 --seqType fq
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20 #end if
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22 #if $inputs.strand.is_strand_specific:
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23 --SS_lib_type $inputs.strand.library_type
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24 #end if
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26 $inputs.jaccard_clip
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27
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28 #else:
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29 --single $inputs.input
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30
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31 #if $inputs.input.is_of_type('fasta'):
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32 --seqType fa
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33 #else:
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34 --seqType fq
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35 #end if
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36
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37 #if $inputs.strand.is_strand_specific:
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38 --SS_lib_type $inputs.strand.library_type
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39 #end if
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40 #end if
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42 $norm
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43
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44 ## Additional parameters.
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45 #if $additional_params.min_contig_length:
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46 --min_contig_length $additional_params.min_contig_length
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47 #end if
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48 #if $additional_params.long_reads:
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49 --long_reads $additional_params.long_reads
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50 #end if
1
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51 #if $additional_params.guided.is_guided == "yes":
0
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52 --genome_guided_bam $additional_params.guided.genome_guided_bam
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53
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54 #if $additional_params.guided.genome_guided_min_coverage:
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55 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
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56 #end if
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57
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58 #if $additional_params.guided.genome_guided_min_reads_per_partition:
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59 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
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60 #end if
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62 #end if
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64 ## CPU and butterfly options.
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65 --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS} --bfly_opts "-V 10 --stderr"
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66
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67 > $trinity_log 2>&1
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68
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69 ]]></command>
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70 <inputs>
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71 <conditional name="inputs">
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72 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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73 <option value="paired">Paired</option>
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74 <option value="single">Single</option>
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75 </param>
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76 <when value="paired">
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77 <param format="fasta,fastqsanger" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
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78 <param format="fasta,fastqsanger" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
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79 <conditional name="strand">
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80 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
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81 <when value="false">
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82 </when>
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83 <when value="true">
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84 <param name="library_type" type="select" label="Strand-specific Library Type">
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85 <option value="FR">Forward-Reverse</option>
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86 <option value="RF">Reverse-Forward</option>
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87 </param>
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88 </when>
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89 </conditional>
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90 <param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/>
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91 <param name="jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="set if you expect high gene density with UTR overlap"/>
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92 </when>
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93 <when value="single">
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94 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
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95 <conditional name="strand">
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96 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
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97 <when value="false">
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98 </when>
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99 <when value="true">
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100 <param name="library_type" type="select" label="Strand-specific Library Type">
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101 <option value="F">F</option>
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102 <option value="R">R</option>
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103 </param>
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104 </when>
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105 </conditional>
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106 </when>
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107 </conditional>
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108
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109 <param name="norm" type="boolean" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
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110
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111 <section name="additional_params" title="Additional Options" expanded="False">
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112 <param name="min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
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113
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114 <conditional name="guided">
1
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115 <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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116 <option value="no">No</option>
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117 <option value="yes">Yes</option>
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118 </param>
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119 <when value="no">
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120 </when>
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121 <when value="yes">
1
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122 <param format="bam" name="genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
0
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123 <param name="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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124 <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
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125 </when>
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126 </conditional>
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127
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128
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129 <param format="fasta" name="long_reads" type="data" 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"/>
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130 </section>
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131 </inputs>
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132 <outputs>
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133 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
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134 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
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135 </outputs>
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136 <tests>
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137 <test>
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138 <param name="paired_or_single" value="paired"/>
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139 <param name="left_input" value="reads.left.fq"/>
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140 <param name="right_input" value="reads.right.fq"/>
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141 <param name="is_strand_specific" value="true"/>
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142 <param name="norm" value="false"/>
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143 <param name="library_type" value="RF"/>
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144 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
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145 </test>
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146 <test>
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147 <param name="paired_or_single" value="paired"/>
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148 <param name="left_input" value="reads.left.fq"/>
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149 <param name="right_input" value="reads.right.fq"/>
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150 <param name="is_strand_specific" value="true"/>
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151 <param name="norm" value="true"/>
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152 <param name="library_type" value="RF"/>
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153 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
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154 </test>
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155 </tests>
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156 <help>
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157 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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158
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159 .. _Trinity: http://trinityrnaseq.github.io
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160 </help>
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161
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162 <citations>
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163 <citation type="doi">doi:10.1038/nbt.1883</citation>
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164 </citations>
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165 </tool>
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166