Mercurial > repos > morinlab > read_counter
changeset 0:cac6401377d2 draft default tip
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/read_counter commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
| author | morinlab |
|---|---|
| date | Tue, 11 Oct 2016 14:29:02 -0400 |
| parents | |
| children | |
| files | read_counter.xml tool_dependencies.xml |
| diffstat | 2 files changed, 45 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/read_counter.xml Tue Oct 11 14:29:02 2016 -0400 @@ -0,0 +1,39 @@ +<tool id="read_counter" name="readCounter" version="0.1.1"> + <description> + Get Binned Read Distribution for a Sequence Alignment File + </description> + <requirements> + <requirement type="package" version="0.1.1">hmmcopy</requirement> + </requirements> + <command> + <![CDATA[ + + ln -s $input_bam input.bam; + ln -s $input_bam.metadata.bam_index input.bam.bai; + + #if $interval + for i in \$( cat $interval ); do + #end if + + readCounter + + #if $interval + -c \$i + #end if + + input.bam >> $output + + #if $interval + ; done + #end if + + ]]> + </command> + <inputs> + <param type="data" format="bam" name="input_bam" label="Specify BAM Alignment File"/> + <param type="data" format="bed,txt" name="interval" label="Specify Interval" optional="true"/> + </inputs> + <outputs> + <data format="wig" name="output"/> + </outputs> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 11 14:29:02 2016 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="hmmcopy" version="0.1.1"> + <repository changeset_revision="5a70f7f0de26" name="package_hmmcopy_0_1_1" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>