view RUST_metafootprints.xml @ 0:f40b0b26e766 default tip

First commit

<tool id="rust_amino1" name="Metafootprint analysis" version="1">
       <description>(Step 1)</description>
    <requirements>
        <requirement type="package" version="0.1.0">RUST</requirement>
        <requirement type="package" version="0.1.18">samtools</requirement>
    </requirements>
            <command> 
                #if str( $metafootprint_type ) == "Nucleotide"
                    python \${RUST_PATH}/RUST_nucleotide.py $input $alignment  $offset $include_lengths $html_file.files_path $html_file $output1
                #end if
                #if str( $metafootprint_type ) == "Codon"
                    python \${RUST_PATH}/RUST_codon.py $input $alignment $offset $include_lengths $html_file.files_path $html_file $output1
                #end if
                #if str( $metafootprint_type ) == "Amino"
                    python \${RUST_PATH}/RUST_amino.py $input $alignment $offset $include_lengths $html_file.files_path $html_file $output1
                #end if                    
                #if str( $metafootprint_type ) == "Dipeptide"
                    python \${RUST_PATH}/RUST_dipeptide.py $input $alignment $offset $include_lengths $html_file.files_path $html_file $output1
                #end if     
                #if str( $metafootprint_type ) == "Tripeptide"
                    python \${RUST_PATH}/RUST_tripeptide.py $input $alignment  $offset $include_lengths $html_file.files_path $html_file $output1
                #end if
                </command>

   <inputs>
     <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="15" 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"/>
     <param name="metafootprint_type" type="select" label="Metafootprint type" help="Sequence features that may influence read density">
        <option value="Nucleotide">Nucleotide</option>
        <option value="Codon">Codon</option>
        <option value="Amino">Amino</option>
        <option value="Dipeptide">Dipeptide</option>
        <option value="Tripeptide">Tripeptide</option>
      </param>
      
   </inputs>
   <outputs>
       <data format="csv" name="output1" label = "$tool.name [$metafootprint_type] on $on_string" />
     <data format="html" name="html_file" label="$tool.name [$metafootprint_type png] on $on_string" >  
     </data>
   </outputs>
 

 
   <help>
**What it does**

This tool produces a RUST metafootprint profile that reveals the influence of mRNA features such as codons/amino acids on the relative read density in the sample across the entire ribosome and nascent peptide region. The Kullback-Leibler divergence across these sites is also provided.

------

**Transcriptome file**

By default the RUST analysis is carried out on the longest ORF in each transcript. Alternatively the user may provide alignments to the entire transcripts with information of both the translation initiation and termination sites. These are to be provided along side the name of each transcript in Transcriptome file. It must be in a tab delimited and in the following format ">transcript name{tab}initiation site coordinate{tab}termination site coordinate". 

The alignments used to produce the RUST values start 120 nucleotides after the start codon and finish 60 nucleotides before the stop codon. Transcripts with ORF length less than 230 nucleotides and those whose reading frame is not divisible by three are ignored.

------

**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>