Mercurial > repos > iuc > trinity
comparison trinity.xml @ 1:0067c78f49dc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1abd7a1cbd25b687267df2ebc4dfba5894797a64
| author | iuc |
|---|---|
| date | Wed, 09 Dec 2015 07:19:52 -0500 |
| parents | 606b7748965d |
| children | de0af39266ef |
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| 0:606b7748965d | 1:0067c78f49dc |
|---|---|
| 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 |