rust_wrapper: RUST_metafootprints.xml annotate

author	Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date	Tue, 20 Oct 2015 13:05:05 +0100
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0 f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	1 <tool id="rust_amino1" name="Metafootprint analysis" version="1">
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	2 <description>(Step 1)</description>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	3 <requirements>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	4 <requirement type="package" version="0.1.0">RUST</requirement>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	5 <requirement type="package" version="0.1.18">samtools</requirement>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	6 </requirements>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	7 <command>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	8 #if str( $metafootprint_type ) == "Nucleotide"
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	9 python \${RUST_PATH}/RUST_nucleotide.py $input $alignment $offset $include_lengths $html_file.files_path $html_file $output1
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	10 #end if
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	11 #if str( $metafootprint_type ) == "Codon"
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	12 python \${RUST_PATH}/RUST_codon.py $input $alignment $offset $include_lengths $html_file.files_path $html_file $output1
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	13 #end if
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	14 #if str( $metafootprint_type ) == "Amino"
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	15 python \${RUST_PATH}/RUST_amino.py $input $alignment $offset $include_lengths $html_file.files_path $html_file $output1
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	16 #end if
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	17 #if str( $metafootprint_type ) == "Dipeptide"
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	18 python \${RUST_PATH}/RUST_dipeptide.py $input $alignment $offset $include_lengths $html_file.files_path $html_file $output1
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	19 #end if
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	20 #if str( $metafootprint_type ) == "Tripeptide"
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	21 python \${RUST_PATH}/RUST_tripeptide.py $input $alignment $offset $include_lengths $html_file.files_path $html_file $output1
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	22 #end if
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	23 </command>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	24
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	25 <inputs>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	26 <param format="fasta" name="input" type="data" label="Transcriptome file" help="A fasta file whose transcripts are used to produce the metafootprint profile."/>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	27 <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."/>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	28 <param name="offset" value="15" type="integer" label="Nucleotide offset to A-site"/>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	29 <param name="include_lengths" type="text"
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	30 label="Lengths of ribosome footprints
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	31 to be included"
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	32 help="Here you can specify the lengths of ribosome footprints to
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	33 be included (28:32 includes reads of length 28,29,30,31,32)."
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	34 value="28:32"/>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	35 <param name="metafootprint_type" type="select" label="Metafootprint type" help="Sequence features that may influence read density">
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	36 <option value="Nucleotide">Nucleotide</option>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	37 <option value="Codon">Codon</option>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	38 <option value="Amino">Amino</option>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	39 <option value="Dipeptide">Dipeptide</option>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	40 <option value="Tripeptide">Tripeptide</option>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	41 </param>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	42
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	43 </inputs>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	44 <outputs>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	45 <data format="csv" name="output1" label = "$tool.name [$metafootprint_type] on $on_string" />
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	46 <data format="html" name="html_file" label="$tool.name [$metafootprint_type png] on $on_string" >
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	47 </data>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	48 </outputs>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	49
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	50
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	51
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	52 <help>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	53 What it does
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	54
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	55 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.
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	56
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	57 ------
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	58
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	59 Transcriptome file
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	60
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	61 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".
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	62
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	63 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.
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	64
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	65 ------
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	66
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	67 Citation
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	68
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	69 Surveying the relative impact of mRNA features on local ribosome profiling read density in 28 datasets.
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	70 Patrick O'Connor, Dmitry Andreev, Pavel Baranov
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	71 bioRxiv doi: http://dx.doi.org/10.1101/018762
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	72
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	73
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	74 </help>
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	75
f40b0b26e766 First commit Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com> parents: diff changeset	76 </tool>

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f40b0b26e766 First commit