Mercurial > repos > nml > find_repeats
changeset 0:7f27672ff880 draft
"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
| author | nml |
|---|---|
| date | Tue, 27 Aug 2019 12:31:52 -0400 |
| parents | |
| children | 7e6be57de1a0 |
| files | find-repeats.xml test-data/find-repeats-input-1.fasta test-data/find-repeats-output-1.tabular |
| diffstat | 3 files changed, 58 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/find-repeats.xml Tue Aug 27 12:31:52 2019 -0400 @@ -0,0 +1,46 @@ +<tool id="findrepeat" name="Find Repeats" version ="1.8.2"> + <description>Identify repeat elements using Mummer</description> + <requirements> + <requirement type="package" version="1.8.2">snvphyl-tools</requirement> + <requirement type="package" version="3.23">mummer</requirement> + </requirements> + <command detect_errors="exit_code"> + find-repeats.pl -l $length -p $pid $fasta > $out + </command> + <inputs> + <param name="fasta" type="data" label="Fasta file" format="fasta"/> + <param name="length" label="Minimum length of repeat region" type="integer" value="150"/> + <param name="pid" label="Minimum PID of repeat region" type="integer" value="90"/> + </inputs> + <outputs> + <data format="tabular" name="out" /> + </outputs> + <tests> + <test> + <param name="length" value="150"/> + <param name="pid" value="90"/> + <param name="fasta" value="find-repeats-input-1.fasta"/> + <output name="out" file="find-repeats-output-1.tabular"/> + </test> + </tests> + + <help> +What it does +============ + +Searches a fasta reference file for repeats. + + +Usage +===== + +**Parameters** + - Fasta file: A fasta reference file to search for repeats. + +**Options** + - Minimum length of repeat region (150). + - Minimum PID of repeat region (90). + </help> +<citations> +</citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/find-repeats-input-1.fasta Tue Aug 27 12:31:52 2019 -0400 @@ -0,0 +1,8 @@ +>A +CCCGCTCGCCACGCTTTGGCCATAGTGCTGCCTTCTACGATGTGTAAACCGTGCAACTTAATGCCATCGGTGCCTACCTT +CAGTACTTGCTGTAACGTGGTGAGGTTTTCAGTGCGCTCTTCACCGGGTAACCCAACAATCAAGTGAGTACACACTTTGA +TACCTAACGCTCTAGCTTTGGCAGTGATCTCTGCGTAGCAGGCAAAATCGTGCCCGCGGTTAATGCGTTTTAAAGTCTGG +>B +CCCGCTCGCCACGCTTTGGCCATAGTGCTGCCTTCTACGATGTGTAAACCGTGCAACTTAATGCCATCGGTGCCTACCTT +CAGTACTTGCTGTAACGTGGTGAGGTTTTCAGTGCGCTCTTCACCGGGTAACCCAACAATCAAGTGAGTACACACTTTGA +TACCTAACGCTCTAGCTTTGGCAGTGATCTCTGCGTAGCAGGCAAAATCGTGCCCGCGGTTAATGCGTTTTAAAGTCTGG