Mercurial > repos > vimalkumarvelayudhan > rust_wrapper
diff synergy_31.xml @ 0:f40b0b26e766 default tip
First commit
| author | Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> |
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| date | Tue, 20 Oct 2015 13:05:05 +0100 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/synergy_31.xml Tue Oct 20 13:05:05 2015 +0100 @@ -0,0 +1,33 @@ +<tool id="synergy_31" name="Synergism detection" version="1"> + <description>(Step 2)</description> + <requirements> + <requirement type="package" version="0.1.0">RUST</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <command>python \${RUST_PATH}/synergy_31.py $observed_amino $observed_tripeptide $output1 </command> + <inputs> + <param format="csv" name="observed_amino" type="data" label="Amino acid metafootprint" help="RUST codon metafootprint analysis"/> + <param format="csv" name="observed_tripeptide" type="data" label="Tripeptide metafootprint" help="RUST tripeptide metafootprint analysis" /> + </inputs> + <outputs> + <data format="csv" name="output1" /> + </outputs> + + + + <help> +**What it does** + +Compares the observed RUST ratios for tripeptides to that expected based on that obtained with amino acids to detect cases of synergism in adjacent residues. Returns a csv file with the best candidates for synergism. + +------ + +**Citation** + +Surveying the relative impact of mRNA features on local ribosome profiling read density in 28 datasets. +Patrick O'Connor, Dmitry Andreev, Pavel Baranov +bioRxiv doi: http://dx.doi.org/10.1101/018762 + + </help> + +</tool>