Mercurial > repos > iuc > trinity_align_and_estimate_abundance

annotate align_and_estimate_abundance.xml @ 6:04bd98a9c751 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
author iuc
date Mon, 28 Aug 2017 16:54:12 -0400
parents be3607a306af
children 3baf18bcf03e
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04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.2">
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2 <description>on a 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 <requirement type="package" version="1.3.0">rsem</requirement>
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8 <requirement type="package" version="1.5.1">express</requirement>
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9 <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 -->
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10 <requirement type="package" version="0.8.1">salmon</requirement>
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11 <requirement type="package" version="0.43.1">kallisto</requirement>
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12 </expand>
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13 <command detect_errors="aggressive"><![CDATA[
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14 ln -f -s '$transcripts' input.fa &&
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16 #if $inputs.paired_or_single == "paired":
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17 #if $inputs.left_input.is_of_type('fasta'):
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18 ln -s '$inputs.left_input' paired_left.fa &&
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19 ln -s '$inputs.right_input' paired_right.fa
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20 #else:
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21 ln -s '$inputs.left_input' paired_left.fq &&
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22 ln -s '$inputs.right_input' paired_right.fq
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23 #end if
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24 #else:
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25 #if $inputs.input.is_of_type('fasta'):
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26 ln -s '$inputs.input' single.fa
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27 #else:
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28 ln -s '$inputs.input' single.fq
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29 #end if
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30 #end if
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32 &&
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33
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34 align_and_estimate_abundance.pl
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35
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36 --transcripts input.fa
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37
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38 --est_method $method.est_method
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39 #if $method.est_method == "RSEM" or $method.est_method == "eXpress":
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40 --aln_method $method.aln_method
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41 #else if $method.est_method == "salmon":
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42 --salmon_idx_type $method.salmon_idx_type
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43 #end if
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44
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45 #if $inputs.paired_or_single == "paired":
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46
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47 #if $inputs.left_input.is_of_type('fasta'):
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48 --left paired_left.fa --right paired_right.fa --seqType fa
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49 #else:
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50 --left paired_left.fq --right paired_right.fq --seqType fq
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51 #end if
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52
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53 #if $inputs.strand.is_strand_specific:
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54 --SS_lib_type $inputs.strand.library_type
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55 #end if
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56
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57 --max_ins_size $inputs.paired_fragment_length
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58
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59 #else:
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60 #if $inputs.input.is_of_type('fasta'):
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61 --single single.fa --seqType fa
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62 #else:
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63 --single single.fq --seqType fq
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64 #end if
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65
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66 #if $inputs.strand.is_strand_specific:
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67 --SS_lib_type $inputs.strand.library_type
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68 #end if
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69 #end if
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70
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71 ## Additional parameters.
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72 #if $additional_params.gene_map.has_gene_map == "no":
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73 --gene_trans_map $additional_params.gene_map.gene_trans_map
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74 #else
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75 --trinity_mode
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76 #end if
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77
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78 --prep_reference
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79
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80 --output_dir output
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81
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82 ## CPU
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83 --thread_count \${GALAXY_SLOTS:-4}
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84 ]]></command>
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85 <inputs>
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86 <param format="fasta" name="transcripts" argument="--transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/>
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87 <conditional name="inputs">
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88 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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89 <option value="paired">Paired</option>
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90 <option value="single">Single</option>
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91 </param>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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92 <when value="paired">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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93 <param format="fasta,fastqsanger" name="left_input" argument="--left" type="data" label="Left/Forward strand reads" help=""/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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94 <param format="fasta,fastqsanger" name="right_input" argument="--right" type="data" label="Right/Reverse strand reads" help=""/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
95 <conditional name="strand">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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96 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
97 <when value="false">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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98 </when>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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99 <when value="true">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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100 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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101 <option value="FR">Forward-Reverse</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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102 <option value="RF">Reverse-Forward</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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103 </param>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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104 </when>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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105 </conditional>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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106 <param name="paired_fragment_length" argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="bowtie -X parameter"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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107 </when>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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108 <when value="single">
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iuc
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109 <param format="fasta,fastqsanger" argument="--single" name="input" type="data" label="Single-end reads" help=""/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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110 <conditional name="strand">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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111 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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112 <when value="false">
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113 </when>
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iuc
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114 <when value="true">
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iuc
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115 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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116 <option value="F">F</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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117 <option value="R">R</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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118 </param>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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119 </when>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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120 </conditional>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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121 </when>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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122 </conditional>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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123
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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124 <conditional name="method">
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125 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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126 <option value="RSEM">RSEM</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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127 <option value="eXpress">eXpress</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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128 <option value="salmon">Salmon</option>
6
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
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129 <option value="kallisto">Kallisto</option>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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130 </param>
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iuc
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131 <when value="RSEM">
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iuc
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132 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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133 <option value="bowtie">Bowtie</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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134 <option value="bowtie2">Bowtie2</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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135 </param>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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136 </when>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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137 <when value="eXpress">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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138 <param type="select" name="aln_method" argument="--aln_method" label="Alignment method">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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139 <option value="bowtie">Bowtie</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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140 <option value="bowtie2">Bowtie2</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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141 </param>
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142 </when>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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143 <when value="salmon">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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144 <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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145 <option value="quasi">Quasi</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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146 <option value="fmd">FMD</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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147 </param>
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148 </when>
6
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iuc
parents: 5
diff changeset
149 <when value="kallisto">
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iuc
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diff changeset
150 </when>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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151 </conditional>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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152
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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153 <section name="additional_params" title="Additional Options" expanded="False">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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154 <conditional name="gene_map">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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155 <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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156 <option value="yes">Yes</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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157 <option value="no">No</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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158 </param>
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iuc
parents:
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159 <when value="yes">
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160 </when>
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iuc
parents:
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161 <when value="no">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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162 <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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163 </when>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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164 </conditional>
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165
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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166 </section>
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167 </inputs>
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168 <outputs>
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169 <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/RSEM.isoforms.results">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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170 <filter>method['est_method'] == "RSEM"</filter>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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171 </data>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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172 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/RSEM.genes.results">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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173 <filter>method['est_method'] == "RSEM"</filter>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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174 </data>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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175
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176 <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/results.xprs">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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177 <filter>method['est_method'] == "eXpress"</filter>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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178 </data>
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179 <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/results.xprs.genes">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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180 <filter>method['est_method'] == "eXpress"</filter>
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181 </data>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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182
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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183 <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
184 <filter>method['est_method'] == "salmon"</filter>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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185 </data>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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186 <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
187 <filter>method['est_method'] == "salmon"</filter>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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188 </data>
6
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
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189
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
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190 <data format="tabular" name="isoforms_counts_kallisto" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/abundance.tsv">
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
191 <filter>method['est_method'] == "kallisto"</filter>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
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192 </data>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
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193 <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/abundance.tsv.genes">
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
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194 <filter>method['est_method'] == "kallisto"</filter>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
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195 </data>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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196 </outputs>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
197 <tests>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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198 <test>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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199 <param name="paired_or_single" value="paired"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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200 <param name="left_input" value="reads.left.fq"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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201 <param name="right_input" value="reads.right.fq"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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202 <param name="transcripts" value="raw/Trinity.fasta"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
203 <param name="library_type" value="RF"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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204 <param name="est_method" value="RSEM"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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205 <param name="aln_method" value="bowtie"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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206 <param name="has_gene_map" value="yes"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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207 <output name="isoforms_counts_rsem">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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208 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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209 <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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210 <has_n_columns n="8" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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211 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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212 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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213 <output name="genes_counts_rsem">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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214 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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215 <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
216 <has_n_columns n="7" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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217 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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218 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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219 </test>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
220 <test>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
221 <param name="paired_or_single" value="paired"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
222 <param name="left_input" value="reads.left.fq"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
223 <param name="right_input" value="reads.right.fq"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
224 <param name="transcripts" value="raw/Trinity.fasta"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
225 <param name="library_type" value="RF"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
226 <param name="est_method" value="RSEM"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
227 <param name="aln_method" value="bowtie2"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
228 <param name="has_gene_map" value="yes"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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diff changeset
229 <output name="isoforms_counts_rsem">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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230 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
231 <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
232 <has_n_columns n="8" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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diff changeset
233 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
234 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
235 <output name="genes_counts_rsem">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
236 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
237 <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
238 <has_n_columns n="7" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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diff changeset
239 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
240 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
241 </test>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
242 <test>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
243 <param name="paired_or_single" value="paired"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
244 <param name="left_input" value="reads.left.fq"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
245 <param name="right_input" value="reads.right.fq"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
246 <param name="transcripts" value="raw/Trinity.fasta"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
247 <param name="library_type" value="RF"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
248 <param name="est_method" value="eXpress"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
249 <param name="aln_method" value="bowtie"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
250 <param name="has_gene_map" value="yes"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
251 <output name="isoforms_counts_express">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
252 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
253 <has_line_matching expression=".*&#009;TRINITY_DN2_c3_g1_i1&#009;.*" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
254 <has_n_columns n="15" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
255 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
256 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
257 <output name="genes_counts_express">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
258 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
259 <has_line_matching expression="NA&#009;TRINITY_DN3_c0_g1.*" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
260 <has_n_columns n="15" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
261 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
262 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
263 </test>
6
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
264 <test>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
265 <param name="paired_or_single" value="paired"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
266 <param name="left_input" value="reads.left.fq"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
267 <param name="right_input" value="reads.right.fq"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
268 <param name="transcripts" value="raw/Trinity.fasta"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
269 <param name="library_type" value="RF"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
270 <param name="est_method" value="salmon"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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271 <param name="aln_method" value="bowtie"/>
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272 <param name="has_gene_map" value="yes"/>
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273 <output name="isoforms_counts_salmon">
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274 <assert_contents>
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275 <has_line_matching expression="TRINITY_DN2_c3_g1_i1&#009;.*" />
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276 <has_n_columns n="5" />
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277 </assert_contents>
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278 </output>
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279 <output name="genes_counts_salmon">
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280 <assert_contents>
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281 <has_line_matching expression="TRINITY_DN3_c0_g1.*" />
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282 <has_n_columns n="5" />
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283 </assert_contents>
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284 </output>
6
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285 </test>
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286 <test>
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287 <param name="paired_or_single" value="paired"/>
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288 <param name="left_input" value="reads.left.fq"/>
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289 <param name="right_input" value="reads.right.fq"/>
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290 <param name="transcripts" value="raw/Trinity.fasta"/>
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291 <param name="library_type" value="RF"/>
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292 <param name="est_method" value="kallisto"/>
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293 <param name="has_gene_map" value="yes"/>
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294 <output name="isoforms_counts_kallisto">
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295 <assert_contents>
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296 <has_line_matching expression="TRINITY_DN1_c0_g1_i1&#009;.*" />
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297 <has_n_columns n="5" />
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298 </assert_contents>
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299 </output>
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300 <output name="genes_counts_kallisto">
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301 <assert_contents>
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302 <has_line_matching expression="TRINITY_DN1_c0_g1&#009;.*" />
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303 <has_n_columns n="5" />
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304 </assert_contents>
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305 </output>
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306 </test>
0
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307 </tests>
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308 <help>
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309 <![CDATA[
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310 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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311 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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312
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313 **Inputs**
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314
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315 It takes as input a transcriptome assembled with Trinity and the reads from a RNASeq sample.
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316 You have to choose between several counting methods.
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317
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318 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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319
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320 =========== ================
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321 gene1 transcript1
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322 ----------- ----------------
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323 gene2 transcript2
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324 =========== ================
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325
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326 **Output**
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327
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328 This tool will produce 2 tabular files, with counts for isoforms and genes respectively. More details on this page:
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329
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330 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
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331
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332
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333 .. _Trinity: http://trinityrnaseq.github.io
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334 ]]>
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335 </help>
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336
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337 <expand macro="citation" />
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338 </tool>