Mercurial > repos > iuc > trinity

annotate align_and_estimate_abundance.xml @ 5:e4a9e0798360 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
author iuc
date Tue, 07 Jun 2016 10:26:04 -0400
parents c7555bc21812
children 1b7800489efb
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1 <tool id="align_and_estimate_abundance" name="Align reads and estimate abundance" version="2.1.1.1">
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2 <description>on a de novo assembly of RNA-Seq data</description>
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3 <requirements>
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4 <requirement type="package" version="2.1.1">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="2.2.6">bowtie2</requirement>
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7 <requirement type="package" version="1.2">samtools</requirement>
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8 <requirement type="package" version="1.2.28">rsem</requirement>
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9 <requirement type="package" version="1.5.1">express</requirement>
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10 </requirements>
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11 <stdio>
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12 <exit_code range="1:"/>
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13 </stdio>
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14 <command><![CDATA[
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15 ln -s $transcripts input.fa
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17 &&
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19 align_and_estimate_abundance.pl
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20
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21 --transcripts input.fa
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23 --est_method $method.est_method
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24 #if $method.est_method == "RSEM" or $method.est_method == "eXpress":
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25 --aln_method $method.aln_method
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26 #end if
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28 #if $inputs.paired_or_single == "paired":
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29 --left $inputs.left_input --right $inputs.right_input
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30
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31 #if $inputs.left_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
2
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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
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41 #else:
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42 --single $inputs.input
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43
2
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44 #if $inputs.input.is_of_type('fasta'):
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45 --seqType fa
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46 #else:
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47 --seqType fq
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48 #end if
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49
2
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50 #if $inputs.strand.is_strand_specific:
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51 --SS_lib_type $inputs.strand.library_type
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52 #end if
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53 #end if
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54
2
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55 --max_ins_size $inputs.paired_fragment_length
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56
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57 ## Additional parameters.
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58 #if $additional_params.gene_map.has_gene_map == "no":
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59 --gene_trans_map $additional_params.gene_map.gene_trans_map
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60 #else
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61 --trinity_mode
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62 #end if
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63
2
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64 --prep_reference
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65
2
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66 --output_dir .
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67
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68 ## CPU
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69 --thread_count \${GALAXY_SLOTS:-4}
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70 ]]></command>
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71 <inputs>
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72 <param format="fasta" name="transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/>
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73 <conditional name="inputs">
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74 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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75 <option value="paired">Paired</option>
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76 <option value="single">Single</option>
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77 </param>
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78 <when value="paired">
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79 <param format="fasta,fastqsanger" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
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80 <param format="fasta,fastqsanger" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
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81 <conditional name="strand">
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82 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
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83 <when value="false">
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84 </when>
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85 <when value="true">
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86 <param name="library_type" type="select" label="Strand-specific Library Type">
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87 <option value="FR">Forward-Reverse</option>
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88 <option value="RF">Reverse-Forward</option>
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89 </param>
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90 </when>
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91 </conditional>
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92 <param name="paired_fragment_length" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/>
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93 </when>
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94 <when value="single">
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95 <param format="fasta,fastqsanger" name="input" type="data" label="Single-end reads" help=""/>
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96 <conditional name="strand">
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97 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
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98 <when value="false">
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99 </when>
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100 <when value="true">
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101 <param name="library_type" type="select" label="Strand-specific Library Type">
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102 <option value="F">F</option>
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103 <option value="R">R</option>
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104 </param>
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105 </when>
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106 </conditional>
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107 </when>
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108 </conditional>
3
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109
2
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110 <conditional name="method">
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111 <param type="select" name="est_method" label="Abundance estimation method">
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112 <option value="RSEM">RSEM</option>
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113 <option value="eXpress">eXpress</option>
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114 </param>
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115 <when value="RSEM">
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116 <param type="select" name="aln_method" label="Alignment method">
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117 <option value="bowtie">Bowtie</option>
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118 <option value="bowtie2">Bowtie2</option>
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119 </param>
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120 </when>
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121 <when value="eXpress">
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iuc
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122 <param type="select" name="aln_method" label="Alignment method">
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iuc
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123 <option value="bowtie">Bowtie</option>
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iuc
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124 <option value="bowtie2">Bowtie2</option>
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125 </param>
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126 </when>
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127 </conditional>
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128
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129 <section name="additional_params" title="Additional Options" expanded="False">
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130 <conditional name="gene_map">
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131 <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed">
3
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132 <option value="yes">Yes</option>
2
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133 <option value="no">No</option>
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134 </param>
3
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135 <when value="yes">
2
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136 </when>
3
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137 <when value="no">
2
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iuc
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138 <param format="tabular" name="gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
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139 </when>
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140 </conditional>
3
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141
2
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142 </section>
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143 </inputs>
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144 <outputs>
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145 <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="RSEM.isoforms.results">
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iuc
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146 <filter>method['est_method'] == "RSEM"</filter>
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iuc
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147 </data>
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148 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="RSEM.genes.results">
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iuc
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149 <filter>method['est_method'] == "RSEM"</filter>
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150 </data>
3
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151
2
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152 <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="results.xprs">
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153 <filter>method['est_method'] == "eXpress"</filter>
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154 </data>
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155 <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="results.xprs.genes">
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iuc
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156 <filter>method['est_method'] == "eXpress"</filter>
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157 </data>
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158 </outputs>
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159 <tests>
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160 <test>
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161 <param name="paired_or_single" value="paired"/>
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162 <param name="left_input" value="reads.left.fq"/>
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163 <param name="right_input" value="reads.right.fq"/>
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164 <param name="transcripts" value="raw/Trinity.fasta"/>
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
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165 <param name="library_type" value="RF"/>
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166 <param name="est_method" value="RSEM"/>
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167 <param name="aln_method" value="bowtie"/>
3
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168 <param name="has_gene_map" value="yes"/>
2
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169 <output name="isoforms_counts_rsem">
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170 <assert_contents>
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171 <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
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172 <has_n_columns n="8" />
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173 </assert_contents>
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174 </output>
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175 <output name="genes_counts_rsem">
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176 <assert_contents>
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177 <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />
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178 <has_n_columns n="7" />
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179 </assert_contents>
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180 </output>
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181 </test>
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182 <test>
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183 <param name="paired_or_single" value="paired"/>
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184 <param name="left_input" value="reads.left.fq"/>
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185 <param name="right_input" value="reads.right.fq"/>
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iuc
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186 <param name="transcripts" value="raw/Trinity.fasta"/>
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187 <param name="library_type" value="RF"/>
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188 <param name="est_method" value="RSEM"/>
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189 <param name="aln_method" value="bowtie2"/>
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190 <param name="has_gene_map" value="yes"/>
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191 <output name="isoforms_counts_rsem">
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192 <assert_contents>
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193 <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
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194 <has_n_columns n="8" />
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195 </assert_contents>
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196 </output>
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197 <output name="genes_counts_rsem">
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198 <assert_contents>
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199 <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />
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200 <has_n_columns n="7" />
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201 </assert_contents>
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202 </output>
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203 </test>
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204 <test>
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205 <param name="paired_or_single" value="paired"/>
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206 <param name="left_input" value="reads.left.fq"/>
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207 <param name="right_input" value="reads.right.fq"/>
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208 <param name="transcripts" value="raw/Trinity.fasta"/>
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209 <param name="library_type" value="RF"/>
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210 <param name="est_method" value="eXpress"/>
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211 <param name="aln_method" value="bowtie"/>
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212 <param name="has_gene_map" value="yes"/>
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213 <output name="isoforms_counts_express">
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214 <assert_contents>
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215 <has_line_matching expression=".*&#009;TRINITY_DN2_c3_g1_i1&#009;.*" />
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216 <has_n_columns n="15" />
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217 </assert_contents>
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218 </output>
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219 <output name="genes_counts_express">
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220 <assert_contents>
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221 <has_line_matching expression="NA&#009;TRINITY_DN3_c0_g1.*" />
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222 <has_n_columns n="15" />
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223 </assert_contents>
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224 </output>
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225 </test>
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226 </tests>
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227 <help>
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228 <![CDATA[
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229 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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230 This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample.
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231
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232 **Inputs**
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233
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234 It takes as input a transcriptome assembled with Trinity and the reads from a RNASeq sample.
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235 You have to choose between several counting methods.
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236
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237 If you dont align on a Trinity assembly, you need to provide a file of the following (tabular) format to map gene ids to transcript ids:
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238
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239 =========== ================
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240 gene1 transcript1
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241 ----------- ----------------
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242 gene2 transcript2
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243 =========== ================
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244
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245 **Output**
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246
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247 This tool will produce 2 tabular files, with counts for isoforms and genes respectively. More details on this page:
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248
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249 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
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250
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251
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252 .. _Trinity: http://trinityrnaseq.github.io
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253 ]]>
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254 </help>
3
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255
2
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256 <citations>
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257 <citation type="doi">10.1038/nbt.1883</citation>
2
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258 </citations>
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259 </tool>
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260