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1 <tool id="fourgamete" name="Four Gamete Test" version="0.1">
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2 <requirements>
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3 <requirement type="package">pysam</requirement>
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4
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4 <requirement type="package">py-popgen</requirement>
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2
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" />
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8 </stdio>
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9 <description>Tests a VCF file for a subregion that passes four gamete test</description>
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10 <command>
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11 <![CDATA[
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8
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12 four_gamete.py
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2
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13 --vcfs $input
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14 --out $output
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15 --4gcompat
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16 --reti
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17 #if str($select_arg) == 'left':
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18 --left
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19 #elif str($select_arg) == 'right':
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20 --right
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21 #elif str($select_arg) == 'randomi':
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22 --rani
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23 #elif str($select_arg) == 'maxlen':
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24 --maxlen
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25 #else:
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26 --ranb
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27 #end if
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28 --numinf $infsites
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29 #if $input.is_of_type('vcf_bgzip')
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30 --tbi $input.metadata.tabix_index
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31 #end if
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32 $ovlps
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33 $ovlpi
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34
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35 ]]>
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36
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37 </command>
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38 <inputs>
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39 <param format="vcf,vcf_bgzip,bcf" name="input" type="data" label="VCF input" />
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40 <param type="integer" name="infsites" label="Number of informative sites required in subregion" value="2" min="0" />
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41 <param name="select_arg" type="select" label="Subregion to Select">
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42 <option value="left">Left-most</option>
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43 <option value="right" selected="True">Right-most</option>
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44 <option value="randomi">Random (equal probability per region)</option>
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45 <option value="randomb">Random (probability equal to size)</option>
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46 <option value="maxlen">Longest Subregion</option>
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47 </param>
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48 <param type="boolean" name="ovlps" truevalue="--ovlps" falsevalue="" label="Include non-informative variants between edge of region and variant that breaks region" />
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49 <param type="boolean" name="ovlpi" truevalue="--ovlpi" falsevalue="" label="Include informative variants from overlapping regions" />
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50 </inputs>
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51 <outputs>
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52 <data format="vcf" name="output"/>
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53 </outputs>
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54 <help>
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55 <![CDATA[
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56
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57 Input VCF will be examined for regions that pass the four-gamete test, which indicates there have been no recombination in this region for this sample. For most cases, a failure of the four-gamete test occurs when two SNPs have four gametes between them. (00,01,10,11) Using selection criteria, a region with the target number of informative SNPs that passes the four-gamete criteria will be output to a VCF file.
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58
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59 ]]>
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60
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61 </help>
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62 </tool>
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