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author bhaas
date Mon, 16 Jul 2012 09:18:23 -0400
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1 <tool id="trinityrnaseq" name="Trinity" version="0.0.1">
2
3 <!-- Written by Jeremy Goecks, now maintained here by bhaas -->
4 <description>De novo assembly of RNA-Seq data Using Trinity</description>
5 <requirements>
6 <requirement type="package">trinity</requirement>
7 </requirements>
8 <command>
9 Trinity.pl --JM $JM --CPU $CPU
10
11 ## Inputs.
12 #if str($inputs.paired_or_single) == "paired":
13 --left $inputs.left_input --right $inputs.right_input
14 #if $inputs.left_input.ext == 'fa':
15 --seqType fa
16 #else:
17 --seqType fq
18 #end if
19 #if str($inputs.library_type) != "None":
20 --SS_lib_type $inputs.library_type
21 #end if
22 --group_pairs_distance $inputs.group_pairs_distance
23 #else:
24 --single $inputs.input
25 #if str($inputs.input.ext) == 'fa':
26 --seqType fa
27 #else:
28 --seqType fq
29 #end if
30 #if str($inputs.library_type) != "None":
31 --SS_lib_type $inputs.library_type
32 #end if
33 #end if
34
35 ## Additional parameters.
36 #if str($additional_params.use_additional) == "yes":
37 --min_kmer_cov $inputs.min_kmer_cov --max_reads_per_graph $inputs.max_reads_per_graph --bflyHeapSpaceMax $input.bflyHeapSpaceMax
38 #if $inputs.bfly_opts != 'None':
39 --bfly_opts " $inputs.bfly_opts "
40 #end if
41 #end if
42
43
44 ## direct to output
45 > $trinity_log 2>&amp;1
46
47 </command>
48 <inputs>
49 <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
50 <option value="1G">1G</option>
51 <option value="10G">10G</option>
52 <option value="50G">50G</option>
53 <option value="100G">100G</option>
54 <option value="200G">200G</option>
55 <option value="500G">500G</option>
56 </param>
57
58 <param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by Trinity" />
59
60
61 <conditional name="inputs">
62 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
63 <option value="paired">Paired</option>
64 <option value="single">Single</option>
65 </param>
66 <when value="paired">
67 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
68 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
69 <param name="library_type" type="select" label="Strand-specific Library Type">
70 <option value="None">None</option>
71 <option value="FR">FR</option>
72 <option value="RF">RF</option>
73 </param>
74 <param name="group_pairs_distance" type="integer" value="500" min="1" label="Group pairs distance" help="Maximum length expected between fragment pairs"/>
75 <param name="path_reinforcement_distance" type="integer" value="75" min="1" label="Path reinforcement distance" help="Minimum read overlap required for path extension in the graph" />
76
77 </when>
78 <when value="single">
79 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
80 <param name="library_type" type="select" label="Strand-specific Library Type">
81 <option value="None">None</option>
82 <option value="F">F</option>
83 <option value="R">R</option>
84 </param>
85 <param name="path_reinforcement_distance" type="integer" value="40" min="1" label="Path reinforcement distance" help="Minimum read overlap required for path extension in the graph" />
86 </when>
87 </conditional>
88
89 <conditional name="additional_params">
90 <param name="use_additional" type="select" label="Use Additional Params?">
91 <option value="no">No</option>
92 <option value="yes">Yes</option>
93 </param>
94 <when value="no">
95 </when>
96 <when value="yes">
97 <param name="min_kmer_cov" type="integer" value="1" min="1" label="inchworm_min_kmer_cov" help="Minimum kmer coverage required by Inchworm for initial contig construction" />
98 <param name="max_reads_per_graph" type="integer" value="20000000" min="10000" label="chrysalis_max_reads_per_graph" help="Maximum number of reads to be anchored within each transcript graph by Chrysalis" />
99
100
101 <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" />
102 <param name="bflyHeapSpaceMax" type="select" label="bflyHeapSpaceMax" help="Java heap space maximum value for Butterfly">
103 <option value="1G">1G</option>
104 <option value="2G">2G</option>
105 <option value="4G" selected="true">4G</option>
106 <option value="10G">10G</option>
107 <option value="20G">20G</option>
108 </param>
109
110 <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
111 </when>
112 </conditional>
113
114
115 </inputs>
116 <outputs>
117 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
118 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
119 </outputs>
120 <tests>
121 </tests>
122 <help>
123 Trinity is a de novo transcript assembler that uses RNA-seq data as input. This tool runs all Trinity_ commands--Inchworm, Chrysalis, and Butterfly--in a single pass.
124
125 .. _Trinity: http://trinityrnaseq.sourceforge.net
126 </help>
127 </tool>