PageRenderTime 22ms CodeModel.GetById 19ms app.highlight 1ms RepoModel.GetById 1ms app.codeStats 0ms

/tools/ngs_rna/trinity_all.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 95 lines | 88 code | 6 blank | 1 comment | 0 complexity | 55cf6cdf53fe365c8ee046cec6e789e9 MD5 | raw file
 1<tool id="trinity_all" name="Trinity" version="0.0.1">
 2    <!-- Supports Trinity r2012-04-22-beta and perhaps a few versions earlier. Wrapper is alpha status. -->
 3    <description>De novo assembly of RNA-Seq data</description>
 4    <requirements>
 5        <requirement type="package">trinity</requirement>
 6    </requirements>
 7    <command>
 8        Trinity.pl 
 9        
10        ## Additional parameters.
11        #if $additional_params.use_additional == "yes":
12            --min_contig_length $additional_params.min_contig_length
13        #end if
14        
15        ## Inputs.
16        #if $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        #else:
24            --single $inputs.input
25            #if  $inputs.input.ext == 'fa':
26                --seqType fa
27            #else:
28                --seqType fq
29            #end if
30        #end if
31
32        #if $strand.is_strand_specific == "yes":
33	    --SS_lib_type $strand.library_type
34        #end if
35        
36        --JM 10G
37
38        ## CPU and butterfly options.
39        --CPU 6 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&amp;1
40    </command>
41    <inputs>
42        <conditional name="inputs">
43            <param name="paired_or_single" type="select" label="Paired or Single-end data?">
44                <option value="paired">Paired</option>
45                <option value="single">Single</option>
46            </param>
47            <when value="paired">
48                <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
49                <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
50                <param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/>
51            </when>
52            <when value="single">
53                <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
54            </when>
55        </conditional>
56	<conditional name="strand">
57	    <param name="is_strand_specific" type="select" label="Is it strand specific data?" help="">
58	    	<option value="no">No</option>
59	    	<option value="yes">Yes</option>
60	    </param>
61	    <when value="no">
62	    </when>
63	    <when value="yes">
64                <param name="library_type" type="select" label="Strand-specific Library Type">
65                    <option value="FR">Forward-Reverse</option>
66                    <option value="RF">Reverse-Forward</option>
67                    <option value="F">Forward</option>
68                    <option value="R">Reverse</option>
69                </param>
70	    </when>
71	</conditional>
72        <conditional name="additional_params">
73            <param name="use_additional" type="select" label="Use Additional Params?">
74                <option value="no">No</option>
75                <option value="yes">Yes</option>
76            </param>
77            <when value="no">
78            </when>
79            <when value="yes">            
80                <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
81            </when>
82        </conditional>
83    </inputs>
84    <outputs>
85        <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
86        <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
87    </outputs>
88    <tests>
89    </tests>
90    <help>
91        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.
92        
93        .. _Trinity: http://trinityrnaseq.sourceforge.net
94    </help>
95</tool>