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comparison trinity.xml @ 3:c7555bc21812 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
author iuc
date Tue, 03 May 2016 10:54:25 -0400
parents de0af39266ef
children e4a9e0798360
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2:de0af39266ef 3:c7555bc21812
1 <tool id="trinity" name="Trinity" version="2.1.1"> 1 <tool id="trinity" name="Trinity" version="2.1.1.1">
2 <description>de novo assembly of RNA-Seq data</description> 2 <description>de novo assembly of RNA-Seq data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1.1">trinity</requirement> 4 <requirement type="package" version="2.1.1">trinity</requirement>
5 <requirement type="package" version="1.1.2">bowtie</requirement> 5 <requirement type="package" version="1.1.2">bowtie</requirement>
6 <requirement type="package" version="1.2">samtools</requirement> 6 <requirement type="package" version="1.2">samtools</requirement>
9 <command><![CDATA[ 9 <command><![CDATA[
10 Trinity 10 Trinity
11 11
12 ## Inputs. 12 ## Inputs.
13 #if $inputs.paired_or_single == "paired": 13 #if $inputs.paired_or_single == "paired":
14 --left $inputs.left_input --right $inputs.right_input 14
15 15 --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) }
16 #if $inputs.left_input.is_of_type('fasta'): 16
17 --right ${ ','.join(['"%s"' % x for x in $inputs.right_input]) }
18
19 #if $inputs.left_input[0].is_of_type('fasta'):
17 --seqType fa 20 --seqType fa
18 #else: 21 #else:
19 --seqType fq 22 --seqType fq
20 #end if 23 #end if
21 24
22 #if $inputs.strand.is_strand_specific: 25 #if $inputs.strand.is_strand_specific:
23 --SS_lib_type $inputs.strand.library_type 26 --SS_lib_type $inputs.strand.library_type
24 #end if 27 #end if
25 28
26 $inputs.jaccard_clip 29 $inputs.jaccard_clip
27 30
28 #else: 31 #else:
29 --single $inputs.input 32 --single ${ ','.join(['"%s"' % x for x in $inputs.input]) }
30 33
31 #if $inputs.input.is_of_type('fasta'): 34 #if $inputs.input[0].is_of_type('fasta'):
32 --seqType fa 35 --seqType fa
33 #else: 36 #else:
34 --seqType fq 37 --seqType fq
35 #end if 38 #end if
36 39
37 #if $inputs.strand.is_strand_specific: 40 #if $inputs.strand.is_strand_specific:
38 --SS_lib_type $inputs.strand.library_type 41 --SS_lib_type $inputs.strand.library_type
39 #end if 42 #end if
40 #end if 43 #end if
41 44
42 $norm 45 $norm
43 46
44 ## Additional parameters. 47 ## Additional parameters.
45 #if $additional_params.min_contig_length: 48 #if $additional_params.min_contig_length:
46 --min_contig_length $additional_params.min_contig_length 49 --min_contig_length $additional_params.min_contig_length
56 #end if 59 #end if
57 60
58 #if $additional_params.guided.genome_guided_min_reads_per_partition: 61 #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 62 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
60 #end if 63 #end if
61 64
62 #end if 65 #end if
63 66
64 ## CPU and butterfly options. 67 ## CPU and butterfly options.
65 --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr" 68 --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr"
66 69
67 ## > $trinity_log 2>&1 70 ## > $trinity_log 2>&1
68 71
69 ]]></command> 72 ]]></command>
70 <inputs> 73 <inputs>
71 <conditional name="inputs"> 74 <conditional name="inputs">
72 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> 75 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
73 <option value="paired">Paired</option> 76 <option value="paired">Paired</option>
74 <option value="single">Single</option> 77 <option value="single">Single</option>
75 </param> 78 </param>
76 <when value="paired"> 79 <when value="paired">
77 <param format="fasta,fastqsanger" name="left_input" type="data" label="Left/Forward strand reads" help=""/> 80 <param format="fasta,fastqsanger" name="left_input" multiple="true" type="data" label="Left/Forward strand reads" help=""/>
78 <param format="fasta,fastqsanger" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> 81 <param format="fasta,fastqsanger" name="right_input" multiple="true" type="data" label="Right/Reverse strand reads" help=""/>
79 <conditional name="strand"> 82 <conditional name="strand">
80 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 83 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
81 <when value="false"> 84 <when value="false">
82 </when> 85 </when>
83 <when value="true"> 86 <when value="true">
88 </when> 91 </when>
89 </conditional> 92 </conditional>
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"/> 93 <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"/>
91 </when> 94 </when>
92 <when value="single"> 95 <when value="single">
93 <param format="fasta,fastqsanger" name="input" type="data" label="Single-end reads" help=""/> 96 <param format="fasta,fastqsanger" name="input" multiple="true" type="data" label="Single-end reads" help=""/>
94 <conditional name="strand"> 97 <conditional name="strand">
95 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 98 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
96 <when value="false"> 99 <when value="false">
97 </when> 100 </when>
98 <when value="true"> 101 <when value="true">
102 </param> 105 </param>
103 </when> 106 </when>
104 </conditional> 107 </conditional>
105 </when> 108 </when>
106 </conditional> 109 </conditional>
107 110
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."/> 111 <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."/>
109 112
110 <section name="additional_params" title="Additional Options" expanded="False"> 113 <section name="additional_params" title="Additional Options" expanded="False">
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"/> 114 <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"/>
112 115
113 <conditional name="guided"> 116 <conditional name="guided">
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"> 117 <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">
115 <option value="no">No</option> 118 <option value="no">No</option>
116 <option value="yes">Yes</option> 119 <option value="yes">Yes</option>
117 </param> 120 </param>
121 <param format="bam" name="genome_guided_bam" type="data" label="Coordinate-sorted BAM file" /> 124 <param format="bam" name="genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
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"/> 125 <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"/>
123 <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/> 126 <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
124 </when> 127 </when>
125 </conditional> 128 </conditional>
126 129
127 130
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"/> 131 <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"/>
129 </section> 132 </section>
130 </inputs> 133 </inputs>
131 <outputs> 134 <outputs>
132 <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /--> 135 <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /-->
133 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> 136 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
134 </outputs> 137 </outputs>
135 <tests> 138 <tests>
136 <test> 139 <test>
137 <param name="paired_or_single" value="paired"/> 140 <param name="paired_or_single" value="paired"/>
138 <param name="left_input" value="reads.left.fq"/> 141 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
139 <param name="right_input" value="reads.right.fq"/> 142 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
140 <param name="is_strand_specific" value="true"/> 143 <param name="is_strand_specific" value="true"/>
141 <param name="norm" value="false"/> 144 <param name="norm" value="false"/>
142 <param name="library_type" value="RF"/> 145 <param name="library_type" value="RF"/>
143 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" /> 146 <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
144 </test> 147 </test>
145 <test> 148 <test>
146 <param name="paired_or_single" value="paired"/> 149 <param name="paired_or_single" value="paired"/>
147 <param name="left_input" value="reads.left.fq"/> 150 <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/>
148 <param name="right_input" value="reads.right.fq"/> 151 <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/>
149 <param name="is_strand_specific" value="true"/> 152 <param name="is_strand_specific" value="true"/>
150 <param name="norm" value="true"/> 153 <param name="norm" value="true"/>
151 <param name="library_type" value="RF"/> 154 <param name="library_type" value="RF"/>
152 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> 155 <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
153 </test> 156 </test>
155 <help> 158 <help>
156 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. 159 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
157 160
158 .. _Trinity: http://trinityrnaseq.github.io 161 .. _Trinity: http://trinityrnaseq.github.io
159 </help> 162 </help>
160 163
161 <citations> 164 <citations>
162 <citation type="doi">doi:10.1038/nbt.1883</citation> 165 <citation type="doi">doi:10.1038/nbt.1883</citation>
163 </citations> 166 </citations>
164 </tool> 167 </tool>
165 168