Mercurial > repos > sjung > bdds
changeset 7:9920c489a5c3 draft
Uploaded
| author | sjung |
|---|---|
| date | Wed, 24 May 2017 00:36:46 -0400 |
| parents | 8dca27fe444a |
| children | 777faad85c7c |
| files | wellington_footprints.xml |
| diffstat | 1 files changed, 34 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wellington_footprints.xml Wed May 24 00:36:46 2017 -0400 @@ -0,0 +1,34 @@ +<tool id="wellington_footprints" name="Wellington Footprints" version="0.2.5"> + <description>accurate identification of digital genomic footprints from DNase-seq data</description> + <requirements> + <requirement type="package">pymodules</requirement> + </requirements> + <command> +#set $final_output = $output.extra_files_path + "/input.bam.input.bed.WellingtonFootprints.FDR.0.01.bed" +mkdir $output.extra_files_path; +ln -s $bam_file input.bam; +ln -s $bam_file.metadata.bam_index input.bam.bai; +ln -s $bed_file input.bed; +wellington_footprints.py input.bed input.bam $output.extra_files_path -fdrlimit $fdrlimit; +cp $final_output $output; +rm -rf $output.extra_files_path + </command> + <stdio> + <exit_code range="1:" level="fatal" description="Error produced" /> + </stdio> + <inputs> + <param help="" format="bam" label="Input BAM" name="bam_file" type="data"/> + <param help="" format="bed" label="Input BED" name="bed_file" type="data"/> + <param help="" label="FDR Limit" value="0" name="fdrlimit" type="integer"/> + </inputs> + + <outputs> + <data format="bed" label="${tool.name} on ${on_string}" name="output" /> + </outputs> + <tests> + <test> + </test> + </tests> + <help> + </help> +</tool>