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author mytest
date Tue, 22 Sep 2015 01:58:00 -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" version="2013_08_14">trinityrnaseq</requirement>
7 <requirement type="package" version="0.1.18">samtools</requirement>
8 <requirement type="package" version="0.12.7">bowtie</requirement>
9 <requirement type="set_environment">TRINITY_HOME</requirement>
10
11 </requirements>
12 <command>
13 \$TRINITY_HOME/Trinity --JM $JM --CPU $CPU
14
15 ## Inputs.
16 #if str($inputs.paired_or_single) == "paired":
17 --left $inputs.left_input --right $inputs.right_input
18 #if $inputs.left_input.ext == 'fa':
19 --seqType fa
20 #else:
21 --seqType fq
22 #end if
23 #if str($inputs.library_type) != "None":
24 --SS_lib_type $inputs.library_type
25 #end if
26 --group_pairs_distance $inputs.group_pairs_distance
27 #else:
28 --single $inputs.input
29 #if str($inputs.input.ext) == 'fa':
30 --seqType fa
31 #else:
32 --seqType fq
33 #end if
34 #if str($inputs.library_type) != "None":
35 --SS_lib_type $inputs.library_type
36 #end if
37 #end if
38
39 ## Additional parameters.
40 #if str($additional_params.use_additional) == "yes":
41 --min_kmer_cov $inputs.min_kmer_cov --max_reads_per_graph $inputs.max_reads_per_graph --bflyHeapSpaceMax $input.bflyHeapSpaceMax
42 #if $inputs.bfly_opts != 'None':
43 --bfly_opts " $inputs.bfly_opts "
44 #end if
45 #end if
46
47
48 ## direct to output
49 > $trinity_log 2>&amp;1
50
51 </command>
52 <inputs>
53 <param name="JM" type="select" label="JM" help="Amount of memory to allocate to Jellyfish for Kmer catalog construction">
54 <option value="1G">1G</option>
55 <option value="10G">10G</option>
56 <option value="50G">50G</option>
57 <option value="100G">100G</option>
58 <option value="200G">200G</option>
59 <option value="500G">500G</option>
60 </param>
61
62 <param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by Trinity" />
63
64
65 <conditional name="inputs">
66 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
67 <option value="paired">Paired</option>
68 <option value="single">Single</option>
69 </param>
70 <when value="paired">
71 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
72 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
73 <param name="library_type" type="select" label="Strand-specific Library Type">
74 <option value="None">None</option>
75 <option value="FR">FR</option>
76 <option value="RF">RF</option>
77 </param>
78 <param name="group_pairs_distance" type="integer" value="500" min="1" label="Group pairs distance" help="Maximum length expected between fragment pairs"/>
79 <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" />
80
81 </when>
82 <when value="single">
83 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
84 <param name="library_type" type="select" label="Strand-specific Library Type">
85 <option value="None">None</option>
86 <option value="F">F</option>
87 <option value="R">R</option>
88 </param>
89 <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" />
90 </when>
91 </conditional>
92
93 <conditional name="additional_params">
94 <param name="use_additional" type="select" label="Use Additional Params?">
95 <option value="no">No</option>
96 <option value="yes">Yes</option>
97 </param>
98 <when value="no">
99 </when>
100 <when value="yes">
101 <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" />
102 <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" />
103
104
105 <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" />
106 <param name="bflyHeapSpaceMax" type="select" label="bflyHeapSpaceMax" help="Java heap space maximum value for Butterfly">
107 <option value="1G">1G</option>
108 <option value="2G">2G</option>
109 <option value="4G" selected="true">4G</option>
110 <option value="10G">10G</option>
111 <option value="20G">20G</option>
112 </param>
113
114 <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
115 </when>
116 </conditional>
117
118
119 </inputs>
120 <outputs>
121 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
122 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
123 </outputs>
124 <tests>
125 </tests>
126 <help>
127 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.
128
129 .. _Trinity: http://trinityrnaseq.sourceforge.net
130 </help>
131 </tool>