view observed_expected.xml @ 0:f40b0b26e766 default tip

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<tool id="plot_RUST_profile" name="Plot transcripts predicted profiles" version="1">
    <description>(Step 4)</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}/observed_expected.py $input $alignment $offset $include_lengths $observed_codon $transcript_name $html_file.files_path $html_file </command>
   <inputs>
       <param name="transcript_name" type="text" size="30"
               label="Name of the transcript to be plotted"
               help="Specific transcript to plot (Use of unique identifier is sufficient for example either '815891337' and 'NM_031946' for 'gi|815891337|ref|NM_031946.6|')">
            <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
            <validator type="empty_field" message="Field requires a value"/>
            <sanitizer>
                <valid>
                    <add value="|"/>
                </valid>
            </sanitizer>
        </param>
        
     <param format="fasta" name="input" type="data" label="Transcriptome file" help="A fasta file whose transcripts are used to produce the metafootprint profile."/>
     <param format="bam" name="alignment" type="data" label="Alignment file" help="The alignments of ribo-seq/mRNA-seq reads to the Transcriptome file. This should be a sorted bam file."/>
     <param name="offset" value="17" type="integer" label="Nucleotide offset to A-site"/>
     <param name="include_lengths" type="text"
               label="Lengths of ribosome footprints
             to be included"
               help="Here you can specify the lengths of ribosome footprints to
             be included (28:32 includes reads of length 28,29,30,31,32)."
              value="28:32">
<!--       <validator type="expression" message="Please input with correct format">len(value.split(':')) == 2</validator> -->
      </param>             
     <param format="csv" name="observed_codon" type="data" label="Codon metafootprint" help="RUST codon metafootprint analysis"/>
   </inputs>

   <outputs>
      <data format="html" name="html_file" label="$tool.name on $on_string" >  
     </data>
   </outputs>
 

 
   <help>
**What it does**

Returns both the observed and and expected profiles for a transcript specified by the user in a csv file. A image of both profiles is provided. The data is provided for 120 nucleotides after the start codon and 60 nucleotides before the stop codon.

------

**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>