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author Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date Tue, 20 Oct 2015 13:05:05 +0100
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2 <tool id="plot_RUST_profile" name="Plot transcripts predicted profiles" version="1">
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3 <description>(Step 4)</description>
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4 <requirements>
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5 <requirement type="package" version="0.1.0">RUST</requirement>
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6 <requirement type="package" version="0.1.18">samtools</requirement>
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7 </requirements>
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8 <command>python \${RUST_PATH}/observed_expected.py $input $alignment $offset $include_lengths $observed_codon $transcript_name $html_file.files_path $html_file </command>
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9 <inputs>
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10 <param name="transcript_name" type="text" size="30"
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11 label="Name of the transcript to be plotted"
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12 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|')">
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13 <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
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14 <validator type="empty_field" message="Field requires a value"/>
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15 <sanitizer>
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16 <valid>
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17 <add value="|"/>
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18 </valid>
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19 </sanitizer>
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20 </param>
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21
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22 <param format="fasta" name="input" type="data" label="Transcriptome file" help="A fasta file whose transcripts are used to produce the metafootprint profile."/>
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23 <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."/>
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24 <param name="offset" value="17" type="integer" label="Nucleotide offset to A-site"/>
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25 <param name="include_lengths" type="text"
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26 label="Lengths of ribosome footprints
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27 to be included"
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28 help="Here you can specify the lengths of ribosome footprints to
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29 be included (28:32 includes reads of length 28,29,30,31,32)."
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30 value="28:32">
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31 <!-- <validator type="expression" message="Please input with correct format">len(value.split(':')) == 2</validator> -->
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32 </param>
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33 <param format="csv" name="observed_codon" type="data" label="Codon metafootprint" help="RUST codon metafootprint analysis"/>
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34 </inputs>
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35
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36 <outputs>
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37 <data format="html" name="html_file" label="$tool.name on $on_string" >
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38 </data>
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39 </outputs>
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43 <help>
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44 **What it does**
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45
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46 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.
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47
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48 ------
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49
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50 **Citation**
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51
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52 Surveying the relative impact of mRNA features on local ribosome profiling read density in 28 datasets.
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53 Patrick O'Connor, Dmitry Andreev, Pavel Baranov
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54 bioRxiv doi: http://dx.doi.org/10.1101/018762
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55
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56 </help>
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57
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58 </tool>