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comparison trinity.xml @ 10:831abd20e690 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
author iuc
date Mon, 01 Aug 2016 14:42:55 -0400
parents e4a9e0798360
children 03884591c766
comparison
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9:8bd817614cc8 10:831abd20e690
1 <tool id="trinity" name="Trinity" version="2.1.1.1"> 1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.0">
2 <description>de novo assembly of RNA-Seq data</description> 2 <description>de novo assembly of RNA-Seq data</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="2.1.1">trinity</requirement> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
5 <requirement type="package" version="1.1.2">bowtie</requirement> 7 <requirement type="package" version="1.1.2">bowtie</requirement>
6 <requirement type="package" version="1.2">samtools</requirement> 8 <requirement type="package" version="1.2">samtools</requirement>
7 <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement> 9 <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement>
8 </requirements> 10 </expand>
11 <expand macro="stdio"/>
9 <command><![CDATA[ 12 <command><![CDATA[
10 Trinity 13 Trinity
11 14
12 ## Inputs. 15 ## Inputs.
13 #if $inputs.paired_or_single == "paired": 16 #if $inputs.paired_or_single == "paired":
62 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition 65 --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
63 #end if 66 #end if
64 67
65 #end if 68 #end if
66 69
70 #if $additional_params.min_kmer_cov:
71 --min_kmer_cov $additional_params.min_kmer_cov
72 #end if
73
67 ## CPU and butterfly options. 74 ## CPU and butterfly options.
68 --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr" 75 --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr"
69 76
70 ## > $trinity_log 2>&1 77 ## > $trinity_log 2>&1
71 78
75 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> 82 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
76 <option value="paired">Paired</option> 83 <option value="paired">Paired</option>
77 <option value="single">Single</option> 84 <option value="single">Single</option>
78 </param> 85 </param>
79 <when value="paired"> 86 <when value="paired">
80 <param format="fasta,fastqsanger" name="left_input" multiple="true" type="data" label="Left/Forward strand reads" help=""/> 87 <param format="fasta,fastqsanger" argument="--left" name="left_input" multiple="true" type="data" label="Left/Forward strand reads" help=""/>
81 <param format="fasta,fastqsanger" name="right_input" multiple="true" type="data" label="Right/Reverse strand reads" help=""/> 88 <param format="fasta,fastqsanger" argument="--right" name="right_input" multiple="true" type="data" label="Right/Reverse strand reads" help=""/>
82 <conditional name="strand"> 89 <conditional name="strand">
83 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 90 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
84 <when value="false"> 91 <when value="false">
85 </when> 92 </when>
86 <when value="true"> 93 <when value="true">
87 <param name="library_type" type="select" label="Strand-specific Library Type"> 94 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
88 <option value="FR">Forward-Reverse</option> 95 <option value="FR">Forward-Reverse</option>
89 <option value="RF">Reverse-Forward</option> 96 <option value="RF">Reverse-Forward</option>
90 </param> 97 </param>
91 </when> 98 </when>
92 </conditional> 99 </conditional>
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"/> 100 <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"/>
94 </when> 101 </when>
95 <when value="single"> 102 <when value="single">
96 <param format="fasta,fastqsanger" name="input" multiple="true" type="data" label="Single-end reads" help=""/> 103 <param format="fasta,fastqsanger" name="input" argument="--single" multiple="true" type="data" label="Single-end reads" help=""/>
97 <conditional name="strand"> 104 <conditional name="strand">
98 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> 105 <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
99 <when value="false"> 106 <when value="false">
100 </when> 107 </when>
101 <when value="true"> 108 <when value="true">
102 <param name="library_type" type="select" label="Strand-specific Library Type"> 109 <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
103 <option value="F">F</option> 110 <option value="F">F</option>
104 <option value="R">R</option> 111 <option value="R">R</option>
105 </param> 112 </param>
106 </when> 113 </when>
107 </conditional> 114 </conditional>
108 </when> 115 </when>
109 </conditional> 116 </conditional>
110 117
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."/> 118 <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."/>
112 119
113 <section name="additional_params" title="Additional Options" expanded="False"> 120 <section name="additional_params" title="Additional Options" expanded="False">
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"/> 121 <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"/>
115 122
116 <conditional name="guided"> 123 <conditional name="guided">
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"> 124 <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">
118 <option value="no">No</option> 125 <option value="no">No</option>
119 <option value="yes">Yes</option> 126 <option value="yes">Yes</option>
120 </param> 127 </param>
121 <when value="no"> 128 <when value="no">
122 </when> 129 </when>
123 <when value="yes"> 130 <when value="yes">
124 <param format="bam" name="genome_guided_bam" type="data" label="Coordinate-sorted BAM file" /> 131 <param format="bam" name="genome_guided_bam" argument="--genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
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"/> 132 <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"/>
126 <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/> 133 <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"/>
127 </when> 134 </when>
128 </conditional> 135 </conditional>
129 136
137 <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"/>
130 138
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"/> 139 <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"/>
132 </section> 140 </section>
133 </inputs> 141 </inputs>
134 <outputs> 142 <outputs>
135 <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /--> 143 <!--data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /-->
136 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> 144 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
159 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. 167 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
160 168
161 .. _Trinity: http://trinityrnaseq.github.io 169 .. _Trinity: http://trinityrnaseq.github.io
162 </help> 170 </help>
163 171
164 <citations> 172 <expand macro="citation" />
165 <citation type="doi">10.1038/nbt.1883</citation>
166 </citations>
167 </tool> 173 </tool>
168