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author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Tue, 20 Oct 2015 13:05:05 +0100
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1 <tool id="synergy_31" name="Synergism detection" version="1">
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2 <description>(Step 2)</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.0">RUST</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 </requirements>
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7 <command>python \${RUST_PATH}/synergy_31.py $observed_amino $observed_tripeptide $output1 </command>
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8 <inputs>
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9 <param format="csv" name="observed_amino" type="data" label="Amino acid metafootprint" help="RUST codon metafootprint analysis"/>
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10 <param format="csv" name="observed_tripeptide" type="data" label="Tripeptide metafootprint" help="RUST tripeptide metafootprint analysis" />
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11 </inputs>
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12 <outputs>
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13 <data format="csv" name="output1" />
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14 </outputs>
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17
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18 <help>
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19 **What it does**
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20
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21 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.
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22
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23 ------
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24
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25 **Citation**
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26
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27 Surveying the relative impact of mRNA features on local ribosome profiling read density in 28 datasets.
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28 Patrick O'Connor, Dmitry Andreev, Pavel Baranov
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29 bioRxiv doi: http://dx.doi.org/10.1101/018762
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30
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31 </help>
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32
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33 </tool>