Mercurial > repos > iuc > trinity

annotate trinity.xml @ 2:de0af39266ef draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
author iuc
date Mon, 25 Apr 2016 10:02:37 -0400
parents 0067c78f49dc
children c7555bc21812
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
parents: 1
diff changeset
1 <tool id="trinity" name="Trinity" version="2.1.1">
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
2 <description>de novo assembly of RNA-Seq data</description>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
3 <requirements>
2
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
parents: 1
diff changeset
4 <requirement type="package" version="2.1.1">trinity</requirement>
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
5 <requirement type="package" version="1.1.2">bowtie</requirement>
1
0067c78f49dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1abd7a1cbd25b687267df2ebc4dfba5894797a64
iuc
parents: 0
diff changeset
6 <requirement type="package" version="1.2">samtools</requirement>
0067c78f49dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1abd7a1cbd25b687267df2ebc4dfba5894797a64
iuc
parents: 0
diff changeset
7 <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement>
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
8 </requirements>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
9 <command><![CDATA[
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
10 Trinity
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
11
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
12 ## Inputs.
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
13 #if $inputs.paired_or_single == "paired":
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
14 --left $inputs.left_input --right $inputs.right_input
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
15
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
16 #if $inputs.left_input.is_of_type('fasta'):
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
17 --seqType fa
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
18 #else:
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
19 --seqType fq
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
20 #end if
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
21
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
22 #if $inputs.strand.is_strand_specific:
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
23 --SS_lib_type $inputs.strand.library_type
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
24 #end if
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
25
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
26 $inputs.jaccard_clip
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
27
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
28 #else:
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
29 --single $inputs.input
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
30
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
31 #if $inputs.input.is_of_type('fasta'):
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
32 --seqType fa
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
33 #else:
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
34 --seqType fq
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
35 #end if
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
36
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
37 #if $inputs.strand.is_strand_specific:
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
38 --SS_lib_type $inputs.strand.library_type
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
39 #end if
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
40 #end if
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
41
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
42 $norm
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
43
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
44 ## Additional parameters.
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
45 #if $additional_params.min_contig_length:
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
46 --min_contig_length $additional_params.min_contig_length
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
47 #end if
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
48 #if $additional_params.long_reads:
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
49 --long_reads $additional_params.long_reads
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
50 #end if
1
0067c78f49dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1abd7a1cbd25b687267df2ebc4dfba5894797a64
iuc
parents: 0
diff changeset
51 #if $additional_params.guided.is_guided == "yes":
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
52 --genome_guided_bam $additional_params.guided.genome_guided_bam
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
53
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
54 #if $additional_params.guided.genome_guided_min_coverage:
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
55 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
56 #end if
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
57
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
58 #if $additional_params.guided.genome_guided_min_reads_per_partition:
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
59 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
60 #end if
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
61
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
62 #end if
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
63
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
64 ## CPU and butterfly options.
2
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
parents: 1
diff changeset
65 --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr"
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
66
2
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
parents: 1
diff changeset
67 ## > $trinity_log 2>&1
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
68
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
69 ]]></command>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
70 <inputs>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
71 <conditional name="inputs">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
72 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
73 <option value="paired">Paired</option>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
74 <option value="single">Single</option>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
75 </param>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
76 <when value="paired">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
77 <param format="fasta,fastqsanger" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
78 <param format="fasta,fastqsanger" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
79 <conditional name="strand">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
80 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
81 <when value="false">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
82 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
83 <when value="true">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
84 <param name="library_type" type="select" label="Strand-specific Library Type">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
85 <option value="FR">Forward-Reverse</option>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
86 <option value="RF">Reverse-Forward</option>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
87 </param>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
88 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
89 </conditional>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
90 <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"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
91 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
92 <when value="single">
2
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
parents: 1
diff changeset
93 <param format="fasta,fastqsanger" name="input" type="data" label="Single-end reads" help=""/>
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
94 <conditional name="strand">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
95 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
96 <when value="false">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
97 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
98 <when value="true">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
99 <param name="library_type" type="select" label="Strand-specific Library Type">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
100 <option value="F">F</option>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
101 <option value="R">R</option>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
102 </param>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
103 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
104 </conditional>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
105 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
106 </conditional>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
107
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
108 <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."/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
109
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
110 <section name="additional_params" title="Additional Options" expanded="False">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
111 <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"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
112
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
113 <conditional name="guided">
1
0067c78f49dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1abd7a1cbd25b687267df2ebc4dfba5894797a64
iuc
parents: 0
diff changeset
114 <param name="is_guided" type="select" label="Use the genome guided mode?" help="If you already mapped the reads to the genome, Trinity can use this information">
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
115 <option value="no">No</option>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
116 <option value="yes">Yes</option>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
117 </param>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
118 <when value="no">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
119 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
120 <when value="yes">
1
0067c78f49dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1abd7a1cbd25b687267df2ebc4dfba5894797a64
iuc
parents: 0
diff changeset
121 <param format="bam" name="genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
122 <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"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
123 <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
124 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
125 </conditional>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
126
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
127
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
128 <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"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
129 </section>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
130 </inputs>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
131 <outputs>
2
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
parents: 1
diff changeset
132 <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /-->
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
133 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
134 </outputs>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
135 <tests>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
136 <test>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
137 <param name="paired_or_single" value="paired"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
138 <param name="left_input" value="reads.left.fq"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
139 <param name="right_input" value="reads.right.fq"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
140 <param name="is_strand_specific" value="true"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
141 <param name="norm" value="false"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
142 <param name="library_type" value="RF"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
143 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
144 </test>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
145 <test>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
146 <param name="paired_or_single" value="paired"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
147 <param name="left_input" value="reads.left.fq"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
148 <param name="right_input" value="reads.right.fq"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
149 <param name="is_strand_specific" value="true"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
150 <param name="norm" value="true"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
151 <param name="library_type" value="RF"/>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
152 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
153 </test>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
154 </tests>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
155 <help>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
156 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
157
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
158 .. _Trinity: http://trinityrnaseq.github.io
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
159 </help>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
160
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
161 <citations>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
162 <citation type="doi">doi:10.1038/nbt.1883</citation>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
163 </citations>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
164 </tool>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
165