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1 <tool id="Codon_analysis" name="Codon_density">
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2 <description>To compare Ribo-seq alignments between two sets of conditions, to determine codon occupancy</description>
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3 <requirements>
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4 <requirement type="package">samtools</requirement>
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5 <requirement type="python-module">matplotlib</requirement>
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6 <requirement type="python-module">numpy</requirement>
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7 <requirement type="python-module">scipy</requirement>
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8 <requirement type="python-module">Bio</requirement>
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9 </requirements>
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10 <command interpreter="python">
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11 get_codon_frequency.py
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12 --gff=$annot
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13 --rep=$replicat_opt['rep']
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14 --cond1 $cond1
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15 --cond2 $cond2
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16 --kmer=$kmer
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17 --asite=$asite
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18 --out $out
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19 --site $site
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20 --hex_col1 $color1
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21 --hex_col2 $color2
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22 --dirout $html_file,$html_file.files_path
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23 #if str( $replicat_opt['rep'] ) == 'yes':
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24 --file1=$file1,$file11
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25 --file2=$file2,$file22
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26 #else
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27 --file1=$file1
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28 --file2=$file2
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29 #end if
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30
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31
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32 </command>
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33
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34 <inputs>
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35 <param name="annot" type="data" label="Reference annotation file (GFF)" format="gff" />
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36 <conditional name="replicat_opt">
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37 <param name="rep" type="select" label="Replicate option">
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38 <option value="yes">Yes (only two replicates by condition)</option>
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39 <option value="no">No</option>
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40 </param>
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41 <when value="yes">
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42 ## Use conditional balise : if rep =yes : 4 files, else 2 files
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43 <param name="file1" type="data" label="First replicate of first condition (Bam file)" format="bam" />
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44 <param name="file11" type="data" label="Second replicate of first condition (Bam file)" format="bam" />
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45 <param name="file2" type="data" label="First replicate of second condition (Bam file)" format="bam" />
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46 <param name="file22" type="data" label="First replicate of second condition (Bam file)" format="bam" />
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47 </when>
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48 <when value="no">
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49 <param name="file1" type="data" label="First Bam file" format="bam" />
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50 <param name="file2" type="data" label="Second Bam File" format="bam" />
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51 </when>
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52 </conditional>
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53 <param name="site" type="select" label="Please choose a ribosomal site for codon analysis">
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54 <option value="A">A</option>
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55 <option value="P">P</option>
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56 <option value="E">E</option>
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57 </param>
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58 <param name="asite" type="integer" label="Off-set from the 5'end of the footprint to the A-site" value ="15" />
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59 <param name="kmer" type="integer" label="Lenght of the best phasing footprints" value ="28" />
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60 <param name="cond1" type="text" size="25" label="Condition one" help="Required even if no replicate" value="cond1"/>
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61 <param name="cond2" type="text" size="25" label="Condition two" help="Required even if no replicate" value="cond2"/>
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62 <param name="color1" type="text" size="50" label="Color for first condition" value ="SkyBlue" help="Enter standard name, hex color string, or rgb code. You can find all colors here : http://pythonhosted.org/ete2/reference/reference_svgcolors.html" />
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63 <param name="color2" type="text" size="50" label="Color for second condition" value ="Plum" help="Enter standard name, hex color string, or rgb code. You can find all colors here : http://pythonhosted.org/ete2/reference/reference_svgcolors.html" />
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64
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65 </inputs>
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66
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67 <outputs>
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68 <data format="csv" name="out" label="Codon analysis output file on ${on_string}"/>
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69 <data format="html" name="html_file" label="Codon analysis results on ${on_string}"/>
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70
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71 </outputs>
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72
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73 <help>
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74
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75 Summary
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76 -------
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77 This tool uses Ribo-seq (BAM file) to determine whether codon occupancy differs between two sets of conditions. For each footprint, the codons at the chosen site are recorded and a histogram displaying all the normalised codon numbers is plotted for both sets of conditions. A second histogram groups together all the codons corresponding to a given amino acid. A chi-squared test is then carried out to determine whether the distribution of the codons used is the same in both sets of conditions.
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78
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79
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80 Output
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81 -------
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82 This tool provides an html file containing graphs and a statistical test result. An additional csv file with codon numbers is provided.
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83
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84
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85 Dependances
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86 ------------
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87
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88 .. class:: warningmark
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89
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90 This tool depends on Python (>=2.7) and following packages : numpy 1.8.0, Biopython 1.58, scipy 0.12.0 and matplotlib 1.3.1. Samtools is used for bam manipulation.
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95
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96
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97
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98
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99
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100 </help>
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101 </tool>
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