Mercurial > repos > iuc > trinity
changeset 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 |
files | tool_dependencies.xml trinity.xml |
diffstat | 2 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- a/tool_dependencies.xml Fri Nov 20 06:50:00 2015 -0500 +++ b/tool_dependencies.xml Wed Dec 09 07:19:52 2015 -0500 @@ -6,8 +6,8 @@ <package name="bowtie" version="1.1.2"> <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <set_environment version="1.0"> <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">--max_memory 30G --bflyHeapSpaceMax 30G</environment_variable>
--- a/trinity.xml Fri Nov 20 06:50:00 2015 -0500 +++ b/trinity.xml Wed Dec 09 07:19:52 2015 -0500 @@ -1,10 +1,10 @@ -<tool id="trinity" name="Trinity" version="2.0.6"> +<tool id="trinity" name="Trinity" version="2.0.6.1"> <description>de novo assembly of RNA-Seq data</description> <requirements> <requirement type="package" version="2.0.6">trinity</requirement> <requirement type="package" version="1.1.2">bowtie</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> - <requirement type="set_environment">TRINITY_MAX_MEMORY</requirement> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement> </requirements> <command><![CDATA[ Trinity @@ -48,7 +48,7 @@ #if $additional_params.long_reads: --long_reads $additional_params.long_reads #end if - #if $additional_params.guided.is_guided == "yes" and $additional_params.guided.genome_guided_bam: + #if $additional_params.guided.is_guided == "yes": --genome_guided_bam $additional_params.guided.genome_guided_bam #if $additional_params.guided.genome_guided_min_coverage: @@ -112,14 +112,14 @@ <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"/> <conditional name="guided"> - <param name="is_guided" type="select" label="Use the genome guided mode?" help=""> + <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"> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> </when> <when value="yes"> - <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"/> + <param format="bam" name="genome_guided_bam" type="data" label="Coordinate-sorted BAM file" /> <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"/> <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/> </when>