Mercurial > repos > bgruening > sailfish
changeset 4:03c74355227f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit edee3afc7d729be9a224d21729bb7490a3761a0e
| author | bgruening |
|---|---|
| date | Sun, 18 Sep 2016 06:05:57 -0400 |
| parents | 85d0d479f05b |
| children | 1b4ed566a41c |
| files | sailfish.xml tool_dependencies.xml |
| diffstat | 2 files changed, 10 insertions(+), 14 deletions(-) [+] |
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--- a/sailfish.xml Mon Dec 21 18:18:03 2015 -0500 +++ b/sailfish.xml Sun Sep 18 06:05:57 2016 -0400 @@ -1,7 +1,8 @@ -<tool id="sailfish" name="Sailfish" version="0.7.6.0"> +<tool id="sailfish" name="Sailfish" version="0.7.6.1"> <description>transcript quantification from RNA-seq data</description> <requirements> <requirement type="package" version="0.7.6">sailfish</requirement> + <requirement type="package" version="1.57.0">boost</requirement> </requirements> <macros> <xml name="strandedness"> @@ -72,7 +73,7 @@ --mates2 ./mate2.$ext --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" #end if - --output ./ + --output ./ $biasCorrect --threads "\${GALAXY_SLOTS:-4}" @@ -117,9 +118,9 @@ </param> </when> <!-- build-in --> <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference transcriptome" /> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference transcriptome" help="in FASTA format" /> <param argument="kmerSize" type="integer" value="21" max="32" label="The size of the k-mer on which the index is built" - help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. + help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be. We generally recommend using a k-mer size of at least 20."/> </when> <!-- history --> @@ -208,6 +209,7 @@ </tests> <help> <![CDATA[ + **What it does** Sailfish is a tool for transcript quantification from RNA-seq data. It @@ -310,18 +312,18 @@ OSR (a stranded paired-end protocol where the reads face away from each other, read1 comes from reverse strand and read2 comes from the forward strand) -.. note:: Correspondence to TopHat library types +.. note:: Correspondence to TopHat library types - The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq + The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq read aligner has a different convention for specifying the format of the library. Below is a table that provides the corresponding sailfish/salmon library format string for each of the potential TopHat library types: - +---------------------+-------------------------+ + +---------------------+-------------------------+ | TopHat | Salmon (and Sailfish) | +=====================+============+============+ - | | Paired-end | Single-end | + | | Paired-end | Single-end | +---------------------+------------+------------+ |``-fr-unstranded`` |``-l IU`` |``-l U`` | +---------------------+------------+------------+
--- a/tool_dependencies.xml Mon Dec 21 18:18:03 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="sailfish" version="0.7.6"> - <repository changeset_revision="04996d8b8587" name="package_sailfish_0_7_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>