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1 <tool id="faCount" name="faCount">
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2 <description> Count base statistics and CpGs in FASTA files.</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">faCount</requirement>
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5 </requirements>
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6 <command>
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7 faCount $summary $dinuc $strands $input > $output
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8 </command>
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9
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10 <inputs>
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11 <param name="input" type="data" format="fasta" label="FASTA file" />
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12 <param name="summary" type="boolean" checked="false" falsevalue="" truevalue="-summary" label="Show only summary statistics" />
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13 <param name="dinuc" type="boolean" checked="false" falsevalue="" truevalue="-dinuc" label="Include statistics on dinucletoide frequencies" />
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14 <param name="strands" type="boolean" checked="false" falsevalue="" truevalue="-strands" label="Count bases on both strands" />
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15 </inputs>
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16
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17 <outputs>
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18 <data format="tabular" name="output" />
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19 </outputs>
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20
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21 <tests>
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22 <test>
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23 <param name="input" value="1.fasta" />
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24 <output name="output" file="2.tabular" />
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25 </test>
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26 <test>
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27 <param name="input" value="1.fasta" />
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28 <param name="summary" value="true" />
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29 <param name="dinuc" value="true" />
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30 <param name="strands" value="true" />
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31 <output name="output" file="3.tabular" />
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32 </test>
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33 </tests>
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34
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35 <help>
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36 **What it does**
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37
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38 faCount_ - Count base statistics and CpGs in FA files.
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39
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40 .. _faCount: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faCount
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41
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42 **Usage**
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43
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44 faCount file(s).fa -summary -dinuc -strands
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45
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46 **Examples**
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47
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48 Example 1::
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49
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50 faCount 1.fasta
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51
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52 #seq len A C G T N cpg
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53 HSFAU1 515 125 138 146 106 0 23
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54 HSFAU2 514 124 138 146 106 0 25
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55 HSFAU3 518 125 139 149 105 0 25
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56 HSFAU4 524 128 142 148 106 0 26
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57 HSFAU5 518 124 138 147 109 0 25
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58 total 2589 626 695 736 532 0 124
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59
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60 Example 2::
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61
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62 faCount 1.fasta -summary
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63
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64 #seq len A C G T N cpg
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65 total 2589 626 695 736 532 0 124
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66 prcnt 1.0 0.2418 0.2684 0.2843 0.2055 0.0000 0.0479
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67
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68 Example 3::
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69
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70 faCount 1.fasta -summary -strands
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71
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72 #seq len A C G T N cpg
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73 total 5178 1158 1431 1431 1158 0 248
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74 prcnt 1.0 0.2236 0.2764 0.2764 0.2236 0.0000 0.0479
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75
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76 </help>
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77
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78 </tool>
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