Mercurial > repos > morinlab > fetch_interval
changeset 0:391b1466cab0 draft
Uploaded
| author | morinlab |
|---|---|
| date | Sun, 04 Dec 2016 18:24:13 -0500 |
| parents | |
| children | 588cdb7e20b2 |
| files | fetch_interval.xml |
| diffstat | 1 files changed, 37 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fetch_interval.xml Sun Dec 04 18:24:13 2016 -0500 @@ -0,0 +1,37 @@ +<tool id="fetch_interval" name="Fetch Interval" version="1.0.0"> + <description> Creates Interval files used to parallelize certain Galaxy Tools </description> + <requirements> + <requirement type="package" version="1.0.0">fetch_interval</requirement> + <requirement type="set_environment">FETCH_REPOSITORY_DIR</requirement> + </requirements> + <command> + <![CDATA[ + + mkdir outputs; + #if $output_option.output_option_selector == "collection": + python \$FETCH_REPOSITORY_DIR/fetch_interval.py --mode by_rname --input $input --order $order --output output.txt --chromosome --group_according_to_largest_chromosome --prefixes_to_ignore GL NC MT; + + #else: + python \$FETCH_REPOSITORY_DIR/fetch_interval.py --mode by_rname --input $input --output $order --chromosome --prefixes_to_ignore GL NC MT; + cat $order > ./outputs/samp1.bed; + + #end if + + ]]> + </command> + <inputs> + <conditional name="output_option"> + <param type="select" name="output_option_selector" label="How to Output?"> + <option value="collection">Collection</option> + <option value="file">Single File</option> + </param> + </conditional> + <param type="data" format="bam" name="input" label="BAM Alignment File" help="Information is pulled from the header, ensure consistent across BAMs"/> + </inputs> + <outputs> + <collection name="list_output" type="list" description="Interval Files"> + <discover_datasets pattern="__name_and_ext__" directory="outputs"/> + </collection> + <data format="txt" name="order"/> + </outputs> +</tool>