annotate trinity.xml @ 16:32b86cd8eb50 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
author iuc
date Mon, 28 Aug 2017 16:53:46 -0400
parents e65e640e6196
children 199aa6821ca5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.0">
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>
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
3 <macros>
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
4 <import>macros.xml</import>
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
5 </macros>
15
e65e640e6196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents: 11
diff changeset
6 <expand macro="requirements" />
e65e640e6196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents: 11
diff changeset
7 <command detect_errors="aggressive"><![CDATA[
e65e640e6196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents: 11
diff changeset
8 Trinity --no_version_check
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
9
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
10 ## Inputs.
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
11 #if $inputs.paired_or_single == "paired":
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
12
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
13 --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) }
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
14
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
15 --right ${ ','.join(['"%s"' % x for x in $inputs.right_input]) }
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
16
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
17 #if $inputs.left_input[0].is_of_type('fasta'):
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
18 --seqType fa
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
19 #else:
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
20 --seqType fq
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
21 #end if
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
22
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
23 #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
24 --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
25 #end if
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
26
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
27 $inputs.jaccard_clip
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
28
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
29 #else:
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
30 --single ${ ','.join(['"%s"' % x for x in $inputs.input]) }
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
31
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
32 #if $inputs.input[0].is_of_type('fasta'):
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
33 --seqType fa
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
34 #else:
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
35 --seqType fq
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
36 #end if
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
37
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
38 #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
39 --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
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 #end if
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
42
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
43 $norm
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
44
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
45 ## Additional parameters.
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
46 #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
47 --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
48 #end if
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
49 #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
50 --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
51 #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
52 #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
53 --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
54
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
55 #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
56 --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
57 #end if
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
58
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
59 #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
60 --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
61 #end if
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
62
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
63 #end if
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
64
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
65 #if $additional_params.min_kmer_cov:
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
66 --min_kmer_cov $additional_params.min_kmer_cov
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
67 #end if
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
68
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
69 ## CPU and butterfly options.
15
e65e640e6196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
iuc
parents: 11
diff changeset
70 --CPU \${GALAXY_SLOTS:-4} --max_memory \${TRINITY_MAX_MEMORY:-1G} --bflyHeapSpaceMax \${TRINITY_MAX_MEMORY:-1G} --bfly_opts '-V 10 --stderr'
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
71
2
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
parents: 1
diff changeset
72 ## > $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
73 ]]></command>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
74 <inputs>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
75 <conditional name="inputs">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
76 <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
77 <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
78 <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
79 </param>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
80 <when value="paired">
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
81 <param format="fasta,fastqsanger" argument="--left" name="left_input" multiple="true" type="data" label="Left/Forward strand reads" help=""/>
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
82 <param format="fasta,fastqsanger" argument="--right" name="right_input" multiple="true" type="data" label="Right/Reverse strand reads" help=""/>
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
83 <conditional name="strand">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
84 <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
85 <when value="false">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
86 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
87 <when value="true">
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
88 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
89 <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
90 <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
91 </param>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
92 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
93 </conditional>
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
94 <param name="jaccard_clip" argument="--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"/>
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
95 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
96 <when value="single">
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
97 <param format="fasta,fastqsanger" name="input" argument="--single" multiple="true" 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
98 <conditional name="strand">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
99 <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
100 <when value="false">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
101 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
102 <when value="true">
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
103 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
104 <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
105 <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
106 </param>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
107 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
108 </conditional>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
109 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
110 </conditional>
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
111
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
112 <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
113
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
114 <section name="additional_params" title="Additional Options" expanded="False">
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
115 <param name="min_contig_length" argument="--min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
116
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
117 <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
118 <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
119 <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
120 <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
121 </param>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
122 <when value="no">
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
123 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
124 <when value="yes">
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
125 <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
126 <param name="genome_guided_min_coverage" argument="--genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
127 <param name="genome_guided_min_reads_per_partition" argument="--genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
128 </when>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
129 </conditional>
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
130
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
131 <param format="fasta" name="long_reads" argument="--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"/>
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
132
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
133 <param name="min_kmer_cov" argument="--min_kmer_cov" type="integer" optional="true" value="1" min="1" label="Minimum count for K-mers to be assembled"/>
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
134 </section>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
135 </inputs>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
136 <outputs>
2
de0af39266ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
iuc
parents: 1
diff changeset
137 <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /-->
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
138 <data format="fasta" name="assembled_transcripts" label="${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
139 </outputs>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
140 <tests>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
141 <test>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
142 <param name="paired_or_single" value="paired"/>
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
143 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
144 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
145 <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
146 <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
147 <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
148 <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
149 </test>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
150 <test>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
151 <param name="paired_or_single" value="paired"/>
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
152 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
153 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
154 <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
155 <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
156 <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
157 <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
158 </test>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
159 </tests>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
160 <help>
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
161 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
162
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
163 .. _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
164 </help>
3
c7555bc21812 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
iuc
parents: 2
diff changeset
165
10
831abd20e690 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
iuc
parents: 5
diff changeset
166 <expand macro="citation" />
0
606b7748965d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
167 </tool>