Mercurial > repos > iuc > trinity
comparison trinity.xml @ 10:831abd20e690 draft
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 |
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| 9:8bd817614cc8 | 10:831abd20e690 |
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| 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 |