comparison synergy_31.xml @ 0:f40b0b26e766 default tip

First commit

0:f40b0b26e766

<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.

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**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>