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1 <tool id="trinityrnaseq" name="Trinity" version="2.4.0">
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2
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3 <!-- Originally written by Jeremy Goecks,
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4 later maintained by (in chronological order)
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5 bhaas, Ben Fulton, Cicada Dennis
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6 -->
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7 <description>De novo assembly of RNA-Seq data using Trinity 2.4.0</description>
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8 <requirements>
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9 <requirement type="package" version="2.4.0">trinity</requirement>
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10 </requirements>
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11 <command>
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12 <![CDATA[
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13 python $__tool_directory__/trinity_wrapper.py --mem_per_cpu 31
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14 --CPU \${GALAXY_SLOTS:-4}
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15 #if str($inputs.paired_or_single) == "paired":
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16 --left $inputs.left_input --right $inputs.right_input
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17 #if $inputs.left_input.ext == 'fasta':
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18 --seqType fa
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19 #else:
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20 --seqType fq
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21 #end if
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22 #else:
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23 --single $inputs.input
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24 #if $inputs.input.ext == 'fasta':
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25 --seqType fa
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26 #else:
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27 --seqType fq
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28 #end if
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29 #end if
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30 ## direct to output
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31 --timing trinity_out_dir/Trinity.timing
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32 --user $__user_id__
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33 --fullpath /N/dc2/scratch/tstrnity/rerun
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34 --dir '$adv.rerundir'
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35 --log $trinity_log
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36
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37 ]]>
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38 </command>
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39 <stdio>
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40 <exit_code range="1:" level="fatal" description="Program failed" />
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41 <exit_code range=":-1" level="fatal" description="DRM killed job" />
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42 </stdio>
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43 <inputs>
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44 <conditional name="inputs">
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45 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
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46 <option value="paired">Paired</option>
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47 <option value="single">Single</option>
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48 </param>
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49 <when value="paired">
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50 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
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51 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
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52 </when>
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53 <when value="single">
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54 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
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55 </when>
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56 </conditional>
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57 <section name="adv" title="Allow Job Rerun" expanded="False">
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58 <param name="rerundir" type="text" size="10" label="To make a job rerunnable, you will need to specify a unique tag to label the job, with no spaces or wierd characters." />
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59 </section>
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60 </inputs>
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61 <outputs>
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62 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
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63 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
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64 </outputs>
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65 <tests>
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66 <!-- Not testing with the following inputs anymore.
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67 <param name="left_input" value="FLI1.left.fq" />
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68 <param name="right_input" value="FLI1.right.fq" />
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69 -->
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70 <test>
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71 <param name="paired_or_single" value="paired" />
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72 <param name="left_input" value="reads.left.simPE.fq" />
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73 <param name="right_input" value="reads.right.simPE.fq" />
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74 <param name="adv.rerundir" value="planemo_test_1" />
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75 <output name="trinity_log" >
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76 <assert_contents>
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77 <has_line_matching expression=".+" />
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78 <has_line line="Trinity exited with status 0" />
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79 </assert_contents>
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80 </output>
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81 <output name="assembled_transcripts" >
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82 <assert_contents>
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83 <has_line_matching expression=".+" />
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84 <has_line_matching expression=">TRINITY.+?len=.+?path=.+" />
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85 </assert_contents>
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86 </output>
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87 </test>
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88 <test>
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89 <param name="paired_or_single" value="paired" />
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90 <param name="left_input" value="Sp.cat_ds_hs.left.fq" />
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91 <param name="right_input" value="Sp.cat_ds_hs.right.fq" />
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92 <param name="adv.rerundir" value="planemo_test_2" />
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93 <!-- Following are not being used in this version of trinity.xml -->
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94 <!--
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95 <param name="paired_or_single" value="paired" />
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96 <param name="left_input" file="cat_Sp.left.fq" />
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97 <param name="right_input" file="cat_Sp.right.fq" />
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98 <param name="JM" value="50G" />
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99 <param name="CPU" value="2" />
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100 <param name="library_type" value="None" />
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101 <param name="group_pairs_distance" value="500" />
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102 <param name="path_reinforcement_distance" va;ue="75" />
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103 <param name="use_additional" value="no" />
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104 -->
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105 <output name="trinity_log" >
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106 <assert_contents>
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107 <has_line_matching expression=".+" />
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108 <has_line line="Trinity exited with status 0" />
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109 </assert_contents>
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110 </output>
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111 <output name="assembled_transcripts" >
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112 <assert_contents>
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113 <has_line_matching expression=".+" />
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114 <has_line_matching expression=">TRINITY.+?len=.+?path=.+" />
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115 </assert_contents>
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116 </output>
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117 </test>
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118 </tests>
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119 <help>
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120 This instance is running Trinity version 2.4.0 and uses the following command:
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121
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122 Trinity --max_memory 240G --CPU 8 --seqType seq_type --single singlefile or --left left_file --right right_file
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123
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124 .. class:: infomark
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125
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126 Trinity_, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. For more information, visit Trinity's wiki page here_.
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127
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128 .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
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129 .. _here: https://github.com/trinityrnaseq/trinityrnaseq/wiki
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130 </help>
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131
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132 <citations>
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133 <citation type="doi">10.1038/nbt.1883</citation>
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134 </citations>
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135
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136 </tool>
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