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1 <tool id='id_align_and_estimate_abundance' name='align_and_estimate_abundance' version='1.0'>
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2
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3 <description>align_and_estimate_abundance</description>
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4
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5 <requirements>
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6 <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
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7 <requirement type="package" version="1.1.17">rsem</requirement>
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8 <requirement type="package" version="1.5.1">eXpress</requirement>
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9 <requirement type="package" version="2.1.0">bowtie2</requirement>
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10 <requirement type="package" version="0.12.7">bowtie</requirement>
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11 <requirement type="package" version="0.1.18">samtools</requirement>
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12 <requirement type="set_environment">TRINITY_HOME</requirement>
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13
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14 </requirements>
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15 <command >perl \$TRINITY_HOME/util/align_and_estimate_abundance.pl
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16 --transcripts $transcripts
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17 --est_method $est_method
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18 --aln_method $aln_method
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19 --prep_reference
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20
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21 ## Inputs.
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22 #if str($reads.paired_or_single) == "paired":
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23
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24 --left $reads.left_input --right $reads.right_input
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25
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26 #if $reads.left_input.ext == 'fa':
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27 --seqType fa
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28 #else:
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29 --seqType fq
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30 #end if
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31
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32 ## Additional parameters.
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33 #if str($reads.optional.use_options) == "yes":
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34
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35 #if str($reads.optional.library_type) != "None":
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36 --SS_lib_type $reads.optional.library_type
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37 #end if
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38
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39
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40
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41 #end if
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42
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43 #else:
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44 --single $reads.input
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45
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46 #if str($reads.input.ext) == 'fa':
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47 --seqType fa
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48 #else:
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49 --seqType fq
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50 #end if
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51
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52 ## Additional parameters.
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53 #if str($reads.optional.use_option) == "yes":
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54
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55 #if str($reads.additional_params.library_type) != "None":
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56 --SS_lib_type $reads.optional.library_type
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57 #end if
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58
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59 #end if
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60 #end if
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61
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62 ## direct to output
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63 > $align_and_estimate_abundance_log 2>&1;samtools sort bowtie.bam bowtie_sorted
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64
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65 </command>
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66
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67 <inputs>
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68
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69 <!-- Required -->
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70 <param name="transcripts" type="data" format="fasta" label="Transcripts [ in fasta format ]" help="--transcripts < string > ; transcript fasta file"/>
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71
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72 <param name="est_method" type="select" display="radio" label="Choose abundance estimation method" help="">
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73 <option value="RSEM" selected="True">RSEM</option>
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74 <option value="eXpress">eXpress</option>
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75 </param>
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76
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77 <param name="aln_method" type="select" display="radio" label="Choose alignment method" help="">
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78 <option value="bowtie" selected="True">bowtie</option>
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79 <option value="bowtie2">bowtie2</option>
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80 </param>
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81
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82 <conditional name="reads">
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83 <param name="paired_or_single" type="select" label="Paired or Single-end reads?">
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84 <option value="paired">Paired</option>
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85 <option value="single">Single</option>
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86 </param>
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87
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88
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89 <when value="paired">
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90 <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
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91 <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
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92
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93 <param name="seqtype" type="select" label="--seqType" help="">
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94 <option value='fq' selected='true'>fastq</option>
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95 <option value='fa'>fasta</option>
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96 </param>
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97
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98 <conditional name='optional'>
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99 <param name='use_options' type='select' label='Use Optional parameters?'>
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100 <option value='no'>NO</option>
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101 <option value='yes'>YES</option>
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102 </param>
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103 <when value='no'/>
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104 <when value='yes'>
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105 <param name="library_type" type="select" label="Strand-specific Library Type">
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106 <option value="None">None</option>
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107 <option value="FR">FR</option>
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108 <option value="RF">RF</option>
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109 </param>
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110
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111
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112
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113 </when>
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114 </conditional>
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115 </when>
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116
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117 <when value="single">
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118 <param format="fastq" name="input" type="data" label="Single-end reads" help=""/>
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119 <param name="seqtype" type="select" label="--seqType" help="">
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120 <option value='fq' selected='true'>fastq</option>
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121 <option value='fa'>fasta</option>
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122 </param>
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123
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124 <conditional name='optional'>
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125 <param name='use_options' type='select' label='Use Optional parameters?'>
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126 <option value='no'>NO</option>
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127 <option value='yes'>YES</option>
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128 </param>
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129 <when value='no'/>
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130 <when value='yes'>
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131 <param name="library_type" type="select" label="Strand-specific Library Type">
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132 <option value="None">None</option>
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133 <option value="F">F</option>
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134 <option value="R">R</option>
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135 </param>
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136 </when>
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137 </conditional>
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138 </when>
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139 </conditional>
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140
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141 </inputs>
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142
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143 <outputs>
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144 <data format="txt" name="align_and_estimate_abundance_log" label="${tool.name} on ${on_string}: log" />
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145 <data format="bam" name="bowtie_bam" label="${tool.name} on ${on_string}: bam" from_work_dir="bowtie_sorted.bam" />
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146 <data format="tabular" name="rsem_isoforms" label="${tool.name} on ${on_string}: isoforms" from_work_dir="RSEM.isoforms.results"/>
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147 <data format="tabular" name="rsem_genes" label="${tool.name} on ${on_string}: genes" from_work_dir="RSEM.genes.results"/>
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148 </outputs>
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149 </tool>
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150
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