| Previous changeset 6:8dca27fe444a (2017-05-24) Next changeset 8:777faad85c7c (2017-05-24) |
|
Commit message:
Uploaded |
|
added:
wellington_footprints.xml |
| b |
| diff -r 8dca27fe444a -r 9920c489a5c3 wellington_footprints.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wellington_footprints.xml Wed May 24 00:36:46 2017 -0400 |
| b |
| @@ -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> |