annotate align_and_estimate_abundance.xml @ 13:6d6b72d14170 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3b8670ad0ce9dd90d6a24429bca131362e56d17d"
author iuc
date Fri, 01 Nov 2019 08:09:49 -0400
parents aed859a021c0
children 56162e446004
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1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@">
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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="1.3.2">rsem</requirement>
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8 <requirement type="package" version="0.46.0">kallisto</requirement>
0
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9 </expand>
5
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10 <command detect_errors="aggressive"><![CDATA[
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11 ln -f -s '$transcripts' input.fa &&
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12
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13 #if $additional_params.gene_map.has_gene_map == "yes":
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14 get_Trinity_gene_to_trans_map.pl input.fa > gene_to_trans.map &&
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15 #else:
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16 ln -f -s '$additional_params.gene_map.gene_trans_map' gene_to_trans.map &&
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17 #end if
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18
0
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19 #if $inputs.paired_or_single == "paired":
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20 #if $inputs.left_input.is_of_type('fasta'):
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21 ln -s '$inputs.left_input' paired_left.fa &&
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22 ln -s '$inputs.right_input' paired_right.fa
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23 #else:
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24 ln -s '$inputs.left_input' paired_left.fq &&
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25 ln -s '$inputs.right_input' paired_right.fq
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26 #end if
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27 #else:
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28 #if $inputs.input.is_of_type('fasta'):
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29 ln -s '$inputs.input' single.fa
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30 #else:
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31 ln -s '$inputs.input' single.fq
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32 #end if
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33 #end if
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34
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35 &&
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36
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37 align_and_estimate_abundance.pl
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38
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39 --transcripts input.fa
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40
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41 --est_method $method.est_method
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42 #if $method.est_method == "RSEM":
0
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43 --aln_method $method.aln_method
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44 #else if $method.est_method == "salmon":
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45 --salmon_idx_type $method.salmon_idx_type
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46 #end if
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47
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48 #if $inputs.paired_or_single == "paired":
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49
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50 #if $inputs.left_input.is_of_type('fasta'):
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51 --left paired_left.fa --right paired_right.fa --seqType fa
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52 #else:
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53 --left paired_left.fq --right paired_right.fq --seqType fq
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54 #end if
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55
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56 #if $inputs.strand.is_strand_specific:
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57 --SS_lib_type $inputs.strand.library_type
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58 #end if
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59
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60 --max_ins_size $inputs.paired_fragment_length
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61
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62 #else:
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63 #if $inputs.input.is_of_type('fasta'):
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64 --single single.fa --seqType fa
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65 #else:
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66 --single single.fq --seqType fq
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67 #end if
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68
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69 #if $inputs.strand.is_strand_specific:
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70 --SS_lib_type $inputs.strand.library_type
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71 #end if
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72 #end if
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73
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74 ## Additional parameters.
10
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75 --gene_trans_map gene_to_trans.map
0
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76
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77 --prep_reference
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78
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79 --output_dir output
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80
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81 ## CPU
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82 --thread_count \${GALAXY_SLOTS:-4}
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83 ]]></command>
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84 <inputs>
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85 <param format="fasta" name="transcripts" argument="--transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/>
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86 <conditional name="inputs">
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87 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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88 <option value="paired">Paired</option>
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89 <option value="single">Single</option>
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90 </param>
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91 <when value="paired">
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92 <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
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93 <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:
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94 <conditional name="strand">
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iuc
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95 <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:
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96 <when value="false">
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97 </when>
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iuc
parents:
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98 <when value="true">
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iuc
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99 <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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100 <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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101 <option value="RF">Reverse-Forward</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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102 </param>
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103 </when>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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104 </conditional>
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105 <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
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106 </when>
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107 <when value="single">
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108 <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
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109 <conditional name="strand">
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110 <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
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111 <when value="false">
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112 </when>
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113 <when value="true">
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114 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
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115 <option value="F">F</option>
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116 <option value="R">R</option>
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117 </param>
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118 </when>
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119 </conditional>
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120 </when>
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121 </conditional>
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122
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123 <conditional name="method">
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124 <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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125 <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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126 <option value="salmon">Salmon</option>
6
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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127 <option value="kallisto">Kallisto</option>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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128 </param>
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129 <when value="RSEM">
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130 <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
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131 <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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132 <option value="bowtie2">Bowtie2</option>
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133 </param>
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134 </when>
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135 <when value="salmon">
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136 <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
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137 <option value="quasi">Quasi</option>
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138 <option value="fmd">FMD</option>
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139 </param>
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140 </when>
6
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parents: 5
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141 <when value="kallisto">
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142 </when>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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143 </conditional>
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144
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145 <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
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146 <conditional name="gene_map">
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147 <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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148 <option value="yes">Yes</option>
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149 <option value="no">No</option>
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150 </param>
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151 <when value="yes">
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152 </when>
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iuc
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153 <when value="no">
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154 <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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155 </when>
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156 </conditional>
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157
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158 </section>
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159 </inputs>
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160 <outputs>
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161 <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/RSEM.isoforms.results">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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162 <filter>method['est_method'] == "RSEM"</filter>
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163 </data>
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164 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/RSEM.genes.results">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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165 <filter>method['est_method'] == "RSEM"</filter>
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166 </data>
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167
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168
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169 <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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170 <filter>method['est_method'] == "salmon"</filter>
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171 </data>
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172 <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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173 <filter>method['est_method'] == "salmon"</filter>
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174 </data>
6
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parents: 5
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175
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176 <data format="tabular" name="isoforms_counts_kallisto" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/abundance.tsv">
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iuc
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177 <filter>method['est_method'] == "kallisto"</filter>
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178 </data>
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179 <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/abundance.tsv.genes">
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180 <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
diff changeset
181 </data>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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182 </outputs>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
183 <tests>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
184 <test>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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185 <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
186 <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
187 <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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188 <param name="transcripts" value="raw/Trinity.fasta"/>
10
afd41a430a76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
189 <param name="gene_to_trans" value="raw/Trinity.map" />
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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190 <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
191 <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
192 <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
193 <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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194 <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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195 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
196 <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
197 <has_n_columns n="8" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
198 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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199 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
200 <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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201 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
202 <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
203 <has_n_columns n="7" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
204 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
205 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
206 </test>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
207 <test>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
208 <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
209 <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
210 <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
211 <param name="transcripts" value="raw/Trinity.fasta"/>
10
afd41a430a76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
212 <param name="gene_to_trans" value="raw/Trinity.map" />
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
213 <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
214 <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
215 <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
216 <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
217 <output name="isoforms_counts_rsem">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
218 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
219 <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
220 <has_n_columns n="8" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
221 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
222 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
223 <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
224 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
225 <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
226 <has_n_columns n="7" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
227 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
228 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
229 </test>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
230 <test>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
231 <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
232 <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
233 <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
234 <param name="transcripts" value="raw/Trinity.fasta"/>
10
afd41a430a76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
235 <param name="gene_to_trans" value="raw/Trinity.map" />
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
236 <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
237 <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:
diff changeset
238 <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
239 <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
240 <output name="isoforms_counts_salmon">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
241 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
242 <has_line_matching expression="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
243 <has_n_columns n="5" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
244 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
245 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
246 <output name="genes_counts_salmon">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
247 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
248 <has_line_matching expression="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
249 <has_n_columns n="5" />
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
250 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
251 </output>
6
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
252 </test>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
253 <test>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
254 <param name="paired_or_single" value="paired"/>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
255 <param name="left_input" value="reads.left.fq"/>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
256 <param name="right_input" value="reads.right.fq"/>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
257 <param name="transcripts" value="raw/Trinity.fasta"/>
10
afd41a430a76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
parents: 7
diff changeset
258 <param name="gene_to_trans" value="raw/Trinity.map" />
6
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
259 <param name="library_type" value="RF"/>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
260 <param name="est_method" value="kallisto"/>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
261 <param name="has_gene_map" value="yes"/>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
262 <output name="isoforms_counts_kallisto">
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
263 <assert_contents>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
264 <has_line_matching expression="TRINITY_DN1_c0_g1_i1&#009;.*" />
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
265 <has_n_columns n="5" />
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
266 </assert_contents>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
267 </output>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
268 <output name="genes_counts_kallisto">
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
269 <assert_contents>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
270 <has_line_matching expression="TRINITY_DN1_c0_g1&#009;.*" />
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
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271 <has_n_columns n="5" />
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272 </assert_contents>
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273 </output>
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274 </test>
0
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275 </tests>
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276 <help>
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277 <![CDATA[
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278 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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279 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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280
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281 **Inputs**
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282
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283 It takes as input a transcriptome assembled with Trinity and the reads from a RNASeq sample.
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284 You have to choose between several counting methods.
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285
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286 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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287
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288 =========== ================
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289 gene1 transcript1
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290 ----------- ----------------
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291 gene2 transcript2
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292 =========== ================
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293
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294 **Output**
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295
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296 This tool will produce 2 tabular files, with counts for isoforms and genes respectively. More details on this page:
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297
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298 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
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299
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300
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301 .. _Trinity: http://trinityrnaseq.github.io
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302 ]]>
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303 </help>
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304
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305 <expand macro="citation" />
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306 </tool>