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comparison trinity.xml @ 0:1d4dd6e51f8c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
author iuc
date Fri, 20 Nov 2015 06:46:48 -0500
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-1:000000000000 0:1d4dd6e51f8c
1 <tool id="trinity" name="Trinity" version="2.0.6">
2 <description>de novo assembly of RNA-Seq data</description>
3 <requirements>
4 <requirement type="package" version="2.0.6">trinity</requirement>
5 <requirement type="package" version="1.1.2">bowtie</requirement>
6 <requirement type="package" version="0.1.19">samtools</requirement>
7 <requirement type="set_environment">TRINITY_MAX_MEMORY</requirement>
8 </requirements>
9 <command><![CDATA[
10 Trinity
11
12 ## Inputs.
13 #if $inputs.paired_or_single == "paired":
14 --left $inputs.left_input --right $inputs.right_input
15
16 #if $inputs.left_input.is_of_type('fasta'):
17 --seqType fa
18 #else:
19 --seqType fq
20 #end if
21
22 #if $inputs.strand.is_strand_specific:
23 --SS_lib_type $inputs.strand.library_type
24 #end if
25
26 $inputs.jaccard_clip
27
28 #else:
29 --single $inputs.input
30
31 #if $inputs.input.is_of_type('fasta'):
32 --seqType fa
33 #else:
34 --seqType fq
35 #end if
36
37 #if $inputs.strand.is_strand_specific:
38 --SS_lib_type $inputs.strand.library_type
39 #end if
40 #end if
41
42 $norm
43
44 ## Additional parameters.
45 #if $additional_params.min_contig_length:
46 --min_contig_length $additional_params.min_contig_length
47 #end if
48 #if $additional_params.long_reads:
49 --long_reads $additional_params.long_reads
50 #end if
51 #if $additional_params.guided.is_guided == "yes" and $additional_params.guided.genome_guided_bam:
52 --genome_guided_bam $additional_params.guided.genome_guided_bam
53
54 #if $additional_params.guided.genome_guided_min_coverage:
55 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
56 #end if
57
58 #if $additional_params.guided.genome_guided_min_reads_per_partition:
59 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
60 #end if
61
62 #end if
63
64 ## CPU and butterfly options.
65 --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS} --bfly_opts "-V 10 --stderr"
66
67 > $trinity_log 2>&1
68
69 ]]></command>
70 <inputs>
71 <conditional name="inputs">
72 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
73 <option value="paired">Paired</option>
74 <option value="single">Single</option>
75 </param>
76 <when value="paired">
77 <param format="fasta,fastqsanger" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
78 <param format="fasta,fastqsanger" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
79 <conditional name="strand">
80 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
81 <when value="false">
82 </when>
83 <when value="true">
84 <param name="library_type" type="select" label="Strand-specific Library Type">
85 <option value="FR">Forward-Reverse</option>
86 <option value="RF">Reverse-Forward</option>
87 </param>
88 </when>
89 </conditional>
90 <param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/>
91 <param name="jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="set if you expect high gene density with UTR overlap"/>
92 </when>
93 <when value="single">
94 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
95 <conditional name="strand">
96 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
97 <when value="false">
98 </when>
99 <when value="true">
100 <param name="library_type" type="select" label="Strand-specific Library Type">
101 <option value="F">F</option>
102 <option value="R">R</option>
103 </param>
104 </when>
105 </conditional>
106 </when>
107 </conditional>
108
109 <param name="norm" type="boolean" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
110
111 <section name="additional_params" title="Additional Options" expanded="False">
112 <param name="min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
113
114 <conditional name="guided">
115 <param name="is_guided" type="select" label="Use the genome guided mode?" help="">
116 <option value="no">No</option>
117 <option value="yes">Yes</option>
118 </param>
119 <when value="no">
120 </when>
121 <when value="yes">
122 <param format="bam" name="genome_guided_bam" type="data" optional="true" label="Genome guided BAM file" help="If you already mapped the reads to the genome, trinity can use this information"/>
123 <param name="genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
124 <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
125 </when>
126 </conditional>
127
128
129 <param format="fasta" name="long_reads" type="data" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
130 </section>
131 </inputs>
132 <outputs>
133 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
134 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
135 </outputs>
136 <tests>
137 <test>
138 <param name="paired_or_single" value="paired"/>
139 <param name="left_input" value="reads.left.fq"/>
140 <param name="right_input" value="reads.right.fq"/>
141 <param name="is_strand_specific" value="true"/>
142 <param name="norm" value="false"/>
143 <param name="library_type" value="RF"/>
144 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
145 </test>
146 <test>
147 <param name="paired_or_single" value="paired"/>
148 <param name="left_input" value="reads.left.fq"/>
149 <param name="right_input" value="reads.right.fq"/>
150 <param name="is_strand_specific" value="true"/>
151 <param name="norm" value="true"/>
152 <param name="library_type" value="RF"/>
153 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
154 </test>
155 </tests>
156 <help>
157 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
158
159 .. _Trinity: http://trinityrnaseq.github.io
160 </help>
161
162 <citations>
163 <citation type="doi">doi:10.1038/nbt.1883</citation>
164 </citations>
165 </tool>
166