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annotate draw_variants.xml @ 36:51cd0307fb70

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Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
parents a631c2f6d913
children
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1 <tool id="gd_draw_variants" name="Draw variants" version="1.1.0">
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2 <description>: show positions of SNVs and unsequenced intervals</description>
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4 <command interpreter="python">
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5 #import json
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6 #import base64
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7 #import zlib
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8 #if $use_snp.choice == '1'
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9 #set $snp_file = $use_snp.snp_input
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10 #set $snp_ext = $use_snp.snp_input.ext
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11 #set $snp_names = $use_snp.snp_input.dataset.metadata.individual_names
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12 #set $snp_colms = $use_snp.snp_input.dataset.metadata.individual_columns
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13 #set $snp_dict = dict(zip($snp_names, $snp_colms))
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14 #set $snp_json = json.dumps($snp_dict, separators=(',',':'))
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15 #set $snp_comp = zlib.compress($snp_json, 9)
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16 #set $snp_arg = base64.b64encode($snp_comp)
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17 #else
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18 #set $snp_file = '/dev/null'
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19 #set $snp_ext = ''
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20 #set $snp_arg = ''
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21 #end if
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22 #if $use_cov.choice == '1'
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23 #set $cov_file = $use_cov.cov_input
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24 #set $cov_ext = $use_cov.cov_input.ext
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25 #set $cov_names = $use_cov.cov_input.dataset.metadata.individual_names
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26 #set $cov_colms = $use_cov.cov_input.dataset.metadata.individual_columns
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27 #set $cov_dict = dict(zip($cov_names, $cov_colms))
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28 #set $cov_json = json.dumps($cov_dict, separators=(',',':'))
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29 #set $cov_comp = zlib.compress($cov_json, 9)
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30 #set $cov_arg = base64.b64encode($cov_comp)
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31 #set $cov_min = $use_cov.min_coverage
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32 #else
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33 #set $cov_file = '/dev/null'
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34 #set $cov_ext = ''
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35 #set $cov_arg = ''
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36 #set $cov_min = 0
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37 #end if
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38 #if $use_indiv.choice == '1'
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39 #set $ind_arg = $use_indiv.indiv_input
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40 #else
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41 #set $ind_arg = '/dev/null'
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42 #end if
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43 draw_variants.py '$snp_file' '$snp_ext' '$snp_arg' '$ind_arg' '$annotation_input' '$cov_file' '$cov_ext' '$cov_arg' '$cov_min' '$output'
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44 </command>
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45
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46 <inputs>
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47 <conditional name="use_snp">
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48 <param name="choice" type="select" format="integer" label="Include SNP/Genotype dataset">
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49 <option value="1" selected="true">yes</option>
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50 <option value="0">no</option>
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51 </param>
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52 <when value="0" />
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53 <when value="1">
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54 <param name="snp_input" type="data" format="gd_snp,gd_genotype" label="SNP/Genotype dataset" />
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55 </when>
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56 </conditional>
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57 <conditional name="use_cov">
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58 <param name="choice" type="select" format="integer" label="Include Coverage dataset">
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59 <option value="1" selected="true">yes</option>
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60 <option value="0">no</option>
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61 </param>
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62 <when value="0" />
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63 <when value="1">
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64 <param name="cov_input" type="data" format="gd_snp,gd_genotype" label="Coverage dataset" />
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65 <param name="min_coverage" type="integer" min="1" value="1" label="Minimum coverage" />
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66 </when>
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67 </conditional>
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68 <conditional name="use_indiv">
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69 <param name="choice" type="select" label="Compute for">
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70 <option value="0" selected="true">All individuals</option>
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71 <option value="1">Individuals in a population</option>
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72 </param>
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73 <when value="0" />
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74 <when value="1">
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75 <param name="indiv_input" type="data" format="gd_indivs" label="Population Individuals" />
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76 </when>
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77 </conditional>
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78 <param name="annotation_input" type="data" format="interval" label="Annotation dataset" />
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79 </inputs>
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81 <outputs>
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82 <data name="output" format="tiff" />
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83 </outputs>
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84
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85 <requirements>
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86 <requirement type="package" version="0.1">gd_c_tools</requirement>
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87 </requirements>
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88
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89 <help>
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90 **What it does**
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91
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92 The user supplies the following:
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93
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94 1. A optional file in gd_genotype or gd_snp format giving the mitochondrial SNPs.
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95 2. An optional gd_genotype file gives the sequence coverage for each individual at each mitochondrial position.
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96 3. The minimum depth of sequence coverage. Positions where an individual has less coverage are ignoried.
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97 4. A set of individuals specified with the "Specify individuals" tool.
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98 5. A file of annotation for the reference mitochondrial sequence.
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99
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100 The program draws a picture indicating the locations of SNPs and the inadequately covered interval.
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101 </help>
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102 </tool>