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comparison trinityrnaseq.xml @ 0:d0c258caafaf draft

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author nate
date Tue, 01 Sep 2015 16:15:38 -0400
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1 <tool id="trinity_psc" name="Trinity" version="0.0.1">
2
3 <!-- Written by Jeremy Goecks, now maintained here by bhaas and additional
4 modifications by Nate Coraor -->
5 <description>(Beta) De novo assembly of RNA-Seq data Using Trinity on PSC's Greenfield</description>
6 <requirements>
7 <!-- These are versions available as modules on Greenfield -->
8 <requirement type="package" version="1.1.1">bowtie</requirement>
9 <requirement type="package" version="1.1">samtools</requirement>
10 <requirement type="package" version="jre7">java</requirement>
11 <requirement type="package" version="2.0.6">trinity</requirement>
12 </requirements>
13 <command>
14 MEM=`expr "\${GALAXY_SLOTS:-15}" \* 50 - 16` ;
15 Trinity --max_memory "\${MEM}G"
16 --CPU "\${GALAXY_SLOTS:-16}"
17 --bflyHeapSpaceMax "\${MEM}G"
18
19 ## Inputs.
20 #if str($inputs.paired_or_single) == "paired":
21 --left $inputs.left_input --right $inputs.right_input
22 #if $inputs.left_input.ext == 'fa':
23 --seqType fa
24 #else:
25 --seqType fq
26 #end if
27 #if str($inputs.library_type) != "undefined":
28 --SS_lib_type $inputs.library_type
29 #end if
30 --group_pairs_distance $inputs.group_pairs_distance
31 #else:
32 --single $inputs.input
33 #if str($inputs.input.ext) == 'fa':
34 --seqType fa
35 #else:
36 --seqType fq
37 #end if
38 #if str($inputs.library_type) != "undefined":
39 --SS_lib_type $inputs.library_type
40 #end if
41 #end if
42
43 ## Additional parameters.
44 #if str($additional_params.use_additional) == "yes":
45 --min_kmer_cov $additional_params.min_kmer_cov --max_reads_per_graph $additional_params.max_reads_per_graph
46 #if $additional_params.bfly_opts != 'None':
47 --bfly_opts " $additional_params.bfly_opts "
48 #end if
49 #end if
50
51 ## direct to output
52 > $trinity_log 2>&amp;1
53
54 ## if Trinity fails, output the end of the log to stderr for Galaxy, and touch the output file for Pulsar
55 || (ec=\$? ; cat $trinity_log >&amp;2 ; mkdir -p trinity_out_dir ; touch trinity_out_dir/Trinity.fasta ; exit \$ec)
56
57 </command>
58 <stdio>
59 <exit_code range="1:" level="fatal" description="Program failed" />
60 <exit_code range=":-1" level="fatal" description="DRM killed job" />
61 </stdio>
62 <inputs>
63 <conditional name="inputs">
64 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
65 <option value="paired">Paired</option>
66 <option value="single">Single</option>
67 </param>
68 <when value="paired">
69 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
70 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
71 <param name="library_type" type="select" label="Strand-specific Library Type">
72 <option value="undefined">Not set</option>
73 <option value="FR">FR</option>
74 <option value="RF">RF</option>
75 </param>
76 <param name="group_pairs_distance" type="integer" value="500" min="1" label="Group pairs distance" help="Maximum length expected between fragment pairs"/>
77 <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" />
78 </when>
79 <when value="single">
80 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
81 <param name="library_type" type="select" label="Strand-specific Library Type">
82 <option value="undefined">Not set</option>
83 <option value="F">F</option>
84 <option value="R">R</option>
85 </param>
86 <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" />
87 </when>
88 </conditional>
89
90 <conditional name="additional_params">
91 <param name="use_additional" type="select" label="Use Additional Params?">
92 <option value="no">No</option>
93 <option value="yes">Yes</option>
94 </param>
95 <when value="no">
96 </when>
97 <when value="yes">
98 <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" />
99 <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" />
100 <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" />
101 <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
102 </when>
103 </conditional>
104 </inputs>
105 <outputs>
106 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
107 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
108 </outputs>
109 <tests>
110 </tests>
111 <help>
112 .. warning:: This version of Trinity, which runs on Greenfield_ at the `Pittsburgh Supercomputing Center`_, is a **beta** version. It may not be possible to rerun the same version of this tool, Trinity itself, or its other dependencies (Bowtie, SAMtools) in the future. **When rerunning this tool on the same data, it should, but cannot be guaranteed to reproduce the exact same results to the level of certainty as other Galaxy tools.**
113
114 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.
115
116 .. _Trinity: http://trinityrnaseq.github.io
117 .. _Pittsburgh Supercomputing Center: http://www.psc.edu
118 .. _Greenfield: http://www.psc.edu/index.php/resources-for-users/computing-resources/greenfield
119 </help>
120 </tool>