Mercurial > repos > nilesh > rnaseqc
changeset 1:e92762563f06
test 1
| author | nilesh |
|---|---|
| date | Fri, 12 Jul 2013 15:42:06 -0500 |
| parents | 84a5563f9839 |
| children | 6f78ab9dad96 |
| files | RNASeQC.xml tool_dependencies.xml |
| diffstat | 2 files changed, 36 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/RNASeQC.xml Fri Jul 12 15:42:06 2013 -0500 @@ -0,0 +1,27 @@ +<tool id="RNASeQC" name="RNASeQC"> + <description>RNASeQC: Quality control metrics for RNA-seq data</description> + <requirements> + <requirement type="package" version="0.6.2">bwa</requirement> + <requirement type="set_environment">RNASEQPATH</requirement> + </requirements> + <command interpreter="java"> +-jar \$RNASEQCPATH/RNASeQC.jar -r $input1 -t $input2 -s "SampleID|$input3|Notes" -o output + </command> + + <inputs> + + <param name="input1" type="data" format="fasta" label="Reference genome"/> + <param name="input2" type="data" format="gtf" label="File Defining transcipts"/> + <param name="input4" type="data" format="bam" label="BAM File"/> + + </inputs> + + <outputs> + <data format="txt" name="output" label="output file" /> + </outputs> + + <help> +This tool computes GC content from a FASTA file. + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jul 12 15:42:06 2013 -0500 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bwa" version="0.6.2"> + <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_bwa_0_6_2" owner="devteam" changeset_revision="0778635a84ba" /> + </package> + <set_environment version="1.0"> + <environment_variable name="RNASEQCPATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> +</tool_dependency>