Mercurial > repos > iuc > trinity_align_and_estimate_abundance

annotate align_and_estimate_abundance.xml @ 22:2fb4ee002432 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ec26c475a013d89b0f973f29250d660e79d4751f
author iuc
date Wed, 20 Sep 2023 14:53:59 +0000
parents b2bbe9a7f1b8
children
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1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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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="bio_tools"/>
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7 <expand macro="requirements">
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8 <requirement type="package" version="1.3.3">rsem</requirement>
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9 </expand>
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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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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 if $inputs.left_input.is_of_type('fastqsanger'):
0
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24 ln -s '$inputs.left_input' paired_left.fq &&
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25 ln -s '$inputs.right_input' paired_right.fq
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26 #else:
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27 ln -s '$inputs.left_input' paired_left.fq.gz &&
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28 ln -s '$inputs.right_input' paired_right.fq.gz
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29 #end if
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30 #else:
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31 #if $inputs.input.is_of_type('fasta'):
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32 ln -s '$inputs.input' single.fa
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33 #else if $inputs.input.is_of_type('fastqsanger'):
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34 ln -s '$inputs.input' single.fq
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35 #else:
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36 ln -s '$inputs.input' single.fq.gz
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37 #end if
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38 #end if
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39
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40 &&
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41
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42 align_and_estimate_abundance.pl
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43
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44 --transcripts input.fa
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45
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46 --est_method $method.est_method
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47 #if $method.est_method == "RSEM":
0
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48 --aln_method $method.aln_method
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49 #end if
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51 #if $inputs.paired_or_single == "paired":
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52
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53 #if $inputs.left_input.is_of_type('fasta'):
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54 --left paired_left.fa --right paired_right.fa --seqType fa
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55 #else if $inputs.left_input.is_of_type('fastqsanger'):
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56 --left paired_left.fq --right paired_right.fq --seqType fq
0
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57 #else:
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58 --left paired_left.fq.gz --right paired_right.fq.gz --seqType fq
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59 #end if
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60
20
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61 #if $inputs.strand.is_strand_specific == 'true':
0
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62 --SS_lib_type $inputs.strand.library_type
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63 #end if
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64
20
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65 --max_ins_size $inputs.max_ins_size
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66
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67 #else:
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68 #if $inputs.input.is_of_type('fasta'):
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69 --single single.fa --seqType fa
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70 #else if $inputs.input.is_of_type('fastqsanger'):
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71 --single single.fq --seqType fq
0
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72 #else:
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73 --single single.fq.gz --seqType fq
0
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74 #end if
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75
20
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76 #if $inputs.strand.is_strand_specific == 'true':
0
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77 --SS_lib_type $inputs.strand.library_type
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78 #end if
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79 #end if
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80
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81 ## Additional parameters.
10
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82 --gene_trans_map gene_to_trans.map
0
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83 --prep_reference
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84 --output_dir output
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85
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86 ## CPU
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87 --thread_count \${GALAXY_SLOTS:-4}
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88 ]]></command>
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89 <inputs>
20
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parents: 18
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90 <param format="fasta" argument="--transcripts" type="data" label="Transcripts" help="de novo assembly of RNA-Seq data"/>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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91 <conditional name="inputs">
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92 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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93 <option value="paired">Paired</option>
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94 <option value="single">Single</option>
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95 </param>
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96 <when value="paired">
20
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parents: 18
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97 <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Left/Forward strand reads" />
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parents: 18
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98 <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger,fastqsanger.gz" label="Right/Reverse strand reads" />
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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99 <conditional name="strand">
20
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parents: 18
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100 <param name="is_strand_specific" type="select" label="Strand specific data">
75f4e1859ed7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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parents: 18
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101 <option value="false">No</option>
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parents: 18
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102 <option value="true">Yes</option>
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parents: 18
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103 </param>
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iuc
parents: 18
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104 <when value="false"/>
0
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105 <when value="true">
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106 <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
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107 <option value="FR">Forward-Reverse</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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108 <option value="RF">Reverse-Forward</option>
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109 </param>
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110 </when>
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111 </conditional>
20
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parents: 18
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112 <param argument="--max_ins_size" type="integer" value="800" min="1" label="Maximum insert size" help="Bowtie -X parameter"/>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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113 </when>
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114 <when value="single">
16
893655fa55f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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parents: 15
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115 <param format="fasta,fastqsanger,fastqsanger.gz" argument="--single" name="input" type="data" label="Single-end reads" help=""/>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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116 <conditional name="strand">
20
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parents: 18
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117 <param name="is_strand_specific" type="select" label="Strand specific data">
75f4e1859ed7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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parents: 18
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118 <option value="false">No</option>
75f4e1859ed7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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parents: 18
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119 <option value="true">Yes</option>
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parents: 18
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120 </param>
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iuc
parents: 18
diff changeset
121 <when value="false"/>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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122 <when value="true">
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123 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
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124 <option value="F">F</option>
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iuc
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125 <option value="R">R</option>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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126 </param>
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127 </when>
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128 </conditional>
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129 </when>
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130 </conditional>
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131
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132 <conditional name="method">
20
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133 <param type="select" argument="--est_method" label="Abundance estimation method">
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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134 <option value="RSEM">RSEM</option>
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135 <option value="salmon">Salmon</option>
6
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parents: 5
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136 <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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137 </param>
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138 <when value="RSEM">
20
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139 <param type="select" argument="--aln_method" label="Alignment method">
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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140 <option value="bowtie">Bowtie</option>
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141 <option value="bowtie2">Bowtie2</option>
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142 </param>
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143 </when>
20
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parents: 18
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144 <when value="salmon"/>
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parents: 18
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145 <when value="kallisto"/>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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146 </conditional>
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147
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148 <section name="additional_params" title="Additional Options" expanded="False">
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149 <conditional name="gene_map">
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150 <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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151 <option value="yes">Yes</option>
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152 <option value="no">No</option>
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153 </param>
20
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parents: 18
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154 <when value="yes" />
0
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155 <when value="no">
20
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156 <param argument="--gene_trans_map" type="data" format="tabular" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
0
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157 </when>
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158 </conditional>
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159 </section>
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160 </inputs>
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161 <outputs>
20
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parents: 18
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162 <data format="tabular" name="isoforms_counts_rsem" label="${tool.name} on ${on_string}: isoforms counts (RSEM)" from_work_dir="output/RSEM.isoforms.results">
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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163 <filter>method['est_method'] == "RSEM"</filter>
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164 </data>
20
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parents: 18
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165 <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts (RSEM)" from_work_dir="output/RSEM.genes.results">
75f4e1859ed7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
iuc
parents: 18
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166 <filter>method['est_method'] == "RSEM"</filter>
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parents: 18
diff changeset
167 </data>
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parents: 18
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168 <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts (Salmon)" from_work_dir="output/quant.sf">
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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169 <filter>method['est_method'] == "salmon"</filter>
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170 </data>
20
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171 <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts (Salmon)" from_work_dir="output/quant.sf.genes">
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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172 <filter>method['est_method'] == "salmon"</filter>
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173 </data>
6
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parents: 5
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174
20
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parents: 18
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175 <data format="tabular" name="isoforms_counts_kallisto" label="${tool.name} on ${on_string}: isoforms counts (Kallisto)" from_work_dir="output/abundance.tsv">
6
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parents: 5
diff changeset
176 <filter>method['est_method'] == "kallisto"</filter>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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177 </data>
20
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178 <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts (Kallisto)" from_work_dir="output/abundance.tsv.genes">
6
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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parents: 5
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179 <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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180 </data>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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181 </outputs>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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182 <tests>
22
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iuc
parents: 21
diff changeset
183 <test expect_num_outputs="2">
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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184 <param name="paired_or_single" value="paired"/>
16
893655fa55f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 15
diff changeset
185 <param name="left_input" value="reads.left.fq.gz"/>
893655fa55f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 15
diff changeset
186 <param name="right_input" value="reads.right.fq.gz"/>
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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187 <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:
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188 <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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189 <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
190 <param name="aln_method" value="bowtie"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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191 <param name="has_gene_map" value="yes"/>
18
00719b8004c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707"
iuc
parents: 17
diff changeset
192 <param name="gene_trans_map" 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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193 <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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194 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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195 <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
196 <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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197 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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198 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
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199 <output name="genes_counts_rsem">
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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200 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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diff changeset
201 <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
202 <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
203 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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204 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
205 </test>
22
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iuc
parents: 21
diff changeset
206 <test expect_num_outputs="2">
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
207 <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
208 <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
209 <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
210 <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
211 <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
212 <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
213 <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
214 <param name="has_gene_map" value="yes"/>
18
00719b8004c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707"
iuc
parents: 17
diff changeset
215 <param name="gene_trans_map" 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
216 <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
217 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
218 <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
219 <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
220 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
221 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
222 <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
223 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
224 <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
225 <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
226 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
227 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
228 </test>
22
2fb4ee002432 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ec26c475a013d89b0f973f29250d660e79d4751f
iuc
parents: 21
diff changeset
229 <test expect_num_outputs="2">
0
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
230 <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
231 <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
232 <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
233 <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
234 <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
235 <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
236 <param name="aln_method" value="bowtie"/>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
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diff changeset
237 <param name="has_gene_map" value="yes"/>
18
00719b8004c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707"
iuc
parents: 17
diff changeset
238 <param name="gene_trans_map" 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
239 <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
240 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
241 <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
242 <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
243 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
244 </output>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
245 <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
246 <assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
247 <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
248 <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
249 </assert_contents>
a21e229da9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents:
diff changeset
250 </output>
6
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
251 </test>
22
2fb4ee002432 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ec26c475a013d89b0f973f29250d660e79d4751f
iuc
parents: 21
diff changeset
252 <test expect_num_outputs="2">
6
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
253 <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
254 <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
255 <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
256 <param name="transcripts" value="raw/Trinity.fasta"/>
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="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
258 <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
259 <param name="has_gene_map" value="yes"/>
18
00719b8004c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707"
iuc
parents: 17
diff changeset
260 <param name="gene_trans_map" 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
261 <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
262 <assert_contents>
04bd98a9c751 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
iuc
parents: 5
diff changeset
263 <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
264 <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
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265 </assert_contents>
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266 </output>
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267 <output name="genes_counts_kallisto">
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268 <assert_contents>
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269 <has_line_matching expression="TRINITY_DN1_c0_g1&#009;.*" />
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270 <has_n_columns n="5" />
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271 </assert_contents>
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272 </output>
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273 </test>
0
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274 </tests>
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275 <help>
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276 <![CDATA[
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277 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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278 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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279
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280 **Inputs**
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281
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282 It takes as input a transcriptome assembled with Trinity and the reads from a RNASeq sample.
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283 You have to choose between several counting methods.
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284
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285 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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286
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287 =========== ================
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288 gene1 transcript1
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289 ----------- ----------------
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290 gene2 transcript2
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291 =========== ================
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292
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293 **Output**
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294
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295 This tool will produce 2 tabular files, with counts for isoforms and genes respectively. More details on this page:
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296
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297 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification
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298
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299
21
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300 .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
0
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301 ]]>
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302 </help>
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303
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304 <expand macro="citation" />
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305 </tool>