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comparison trinity.xml @ 1:fd94a21c2131 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1abd7a1cbd25b687267df2ebc4dfba5894797a64
author iuc
date Wed, 09 Dec 2015 07:17:55 -0500
parents 1d4dd6e51f8c
children 1317615eff73
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0:1d4dd6e51f8c 1:fd94a21c2131
1 <tool id="trinity" name="Trinity" version="2.0.6"> 1 <tool id="trinity" name="Trinity" version="2.0.6.1">
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="2.0.6">trinity</requirement> 4 <requirement type="package" version="2.0.6">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="0.1.19">samtools</requirement> 6 <requirement type="package" version="1.2">samtools</requirement>
7 <requirement type="set_environment">TRINITY_MAX_MEMORY</requirement> 7 <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement>
8 </requirements> 8 </requirements>
9 <command><![CDATA[ 9 <command><![CDATA[
10 Trinity 10 Trinity
11 11
12 ## Inputs. 12 ## Inputs.
46 --min_contig_length $additional_params.min_contig_length 46 --min_contig_length $additional_params.min_contig_length
47 #end if 47 #end if
48 #if $additional_params.long_reads: 48 #if $additional_params.long_reads:
49 --long_reads $additional_params.long_reads 49 --long_reads $additional_params.long_reads
50 #end if 50 #end if
51 #if $additional_params.guided.is_guided == "yes" and $additional_params.guided.genome_guided_bam: 51 #if $additional_params.guided.is_guided == "yes":
52 --genome_guided_bam $additional_params.guided.genome_guided_bam 52 --genome_guided_bam $additional_params.guided.genome_guided_bam
53 53
54 #if $additional_params.guided.genome_guided_min_coverage: 54 #if $additional_params.guided.genome_guided_min_coverage:
55 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage 55 --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
56 #end if 56 #end if
110 110
111 <section name="additional_params" title="Additional Options" expanded="False"> 111 <section name="additional_params" title="Additional Options" expanded="False">
112 <param name="min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/> 112 <param name="min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
113 113
114 <conditional name="guided"> 114 <conditional name="guided">
115 <param name="is_guided" type="select" label="Use the genome guided mode?" help=""> 115 <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">
116 <option value="no">No</option> 116 <option value="no">No</option>
117 <option value="yes">Yes</option> 117 <option value="yes">Yes</option>
118 </param> 118 </param>
119 <when value="no"> 119 <when value="no">
120 </when> 120 </when>
121 <when value="yes"> 121 <when value="yes">
122 <param format="bam" name="genome_guided_bam" type="data" optional="true" label="Genome guided BAM file" help="If you already mapped the reads to the genome, trinity can use this information"/> 122 <param format="bam" name="genome_guided_bam" type="data" label="Coordinate-sorted BAM file" />
123 <param name="genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/> 123 <param name="genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
124 <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/> 124 <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
125 </when> 125 </when>
126 </conditional> 126 </conditional>
127 127