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1 <tool id="gd_find_intervals" name="Find remarkable" version="1.0.0">
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2 <description>genomic intervals</description>
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3
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4 <command interpreter="python">
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5 find_intervals.py "$input" "$input.metadata.dbkey" "$output" "$output.files_path"
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6
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7 #if $override_metadata.choice == "0"
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8 "$input.metadata.ref" "$input.metadata.rPos"
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9 #else
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10 "$override_metadata.ref_col" "$override_metadata.rpos_col"
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11 #end if
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12
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13 "$score_col" "$shuffles"
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14
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15 #if $cutoff.type == 'percentage'
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16 "$cutoff.cutoff_pct"
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17 #else
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18 "=$cutoff.cutoff_val"
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19 #end if
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20
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21 "$out_format"
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22 </command>
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23
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24 <inputs>
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25 <param name="input" type="data" format="tabular" label="Input">
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26 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
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27 </param>
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28
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29 <param name="score_col" type="data_column" data_ref="input" numerical="true" label="Column with score"/>
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30
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31 <conditional name="cutoff">
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32 <param name="type" type="select" label="Cutoff type">
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33 <option value="percentage">percentage</option>
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34 <option value="value">value</option>
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35 </param>
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36 <when value="percentage">
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37 <param name="cutoff_pct" type="float" value="95" min="0" max="100" label="Percentage cutoff"/>
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38 </when>
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39 <when value="value">
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40 <param name="cutoff_val" type="float" value="0.0" label="Value cutoff"/>
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41 </when>
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42 </conditional>
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43
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44 <param name="shuffles" type="integer" min="0" value="0" label="Number of randomizations"/>
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45
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46 <param name="out_format" type="select" format="integer" label="Report SNPs">
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47 <option value="0" selected="true">No</option>
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48 <option value="1">Yes</option>
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49 </param>
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50
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51 <conditional name="override_metadata">
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52 <param name="choice" type="select" format="integer" label="Choose columns">
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53 <option value="0" selected="true">No, get columns from metadata</option>
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54 <option value="1" >Yes, choose columns</option>
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55 </param>
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56 <when value="0" />
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57 <when value="1">
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58 <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome"/>
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59 <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position"/>
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60 </when>
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61 </conditional>
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62 </inputs>
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63
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64 <outputs>
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65 <data name="output" format="interval">
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66 <change_format>
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67 <when input="out_format" value="1" format="bigwigpos" />
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68 </change_format>
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69 </data>
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70 </outputs>
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71
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72 <tests>
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73 <test>
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74 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
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75 <param name="score_col" value="5" />
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76 <param name="type" value="value" />
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77 <param name="cutoff_val" value="700.0" />
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78 <param name="shuffles" value="10" />
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79 <param name="out_format" value="0" />
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80 <param name="choice" value="0" />
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81
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82 <output name="output" file="test_out/find_intervals/find_intervals.interval" />
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83 </test>
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84 </tests>
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85
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86 <help>
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87 **What it does**
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88
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89 The user selects a SNP table and specifies the columns containing (1)
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90 chromosome, (2) position, (3) scores (such as an Fst-value for the SNP), (4)
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91 a percentage or raw score for the "cutoff" and (5) the number of times the
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92 data should be randomized (only intervals with score exceeding the maximum for
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93 the randomized data are reported). If a percentage (e.g. 95%) is specified
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94 for #3, then that percentile of the scores is used as the cutoff; this may
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95 not work well if many SNPs have the same score. The program subtracts the
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96 cutoff from every score, then finds genomic intervals (i.e., consecutive runs
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97 of SNPs) whose total score cannot be increased by adding or subtracting one
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98 or more SNPs at the ends of the interval.
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99 </help>
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100 </tool>
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