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1 <tool id="consolidate_fitnesses" name="Consolidate Fitnesses">
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2 <description>of transposon insertion locations</description>
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3 <requirements>
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4 <requirement type="package" version="1.64">biopython</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 consol_fit.py
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8 -i $input
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9 -calctxt $calctxt
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10 -out $output
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11 -out2 $output2
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12 -maxweight $maxweight
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13 -cutoff $cutoff
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14 -cutoff2 $cutoff2
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15 -wig $output3
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16 #if $normalization.calculations == "yes":
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17 -normalize $normalization.genes
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18 #end if
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19 #if $multiply.choice == "yes":
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20 -multiply $multiply.factor
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21 #end if
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22 #if $reads.downstream == "yes":
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23 -d 1
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24 #end if
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25 </command>
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26 <inputs>
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27 <param name="input" type="data" label="Fitness file"/>
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28 <param name="calctxt" type="data" label="the txt file output from calc_fitness"/>
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29 <conditional name="normalization">
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30 <param name="calculations" type="select" label="Normalize fitness calculations?">
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31 <option value="no">No</option>
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32 <option value="yes">Yes</option>
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33 </param>
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34 <when value="no">
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35 <!-- do nothing -->
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36 </when>
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37 <when value="yes">
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38 <param name="genes" type="data" label="Genes to normalize by" />
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39 </when>
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40 </conditional>
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41 <param name="cutoff" type="float" value="0.0" label="Cutoff"/>
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42 <param name="cutoff2" type="float" value="0.0" label="Cutoff2"/>
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43 <param name="maxweight" type="float" value="75" label="Maximum weight of a transposon gene in normalization calculations"/>
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44 <conditional name="multiply">
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45 <param name="choice" type="select" label="Multiply fitness scores by a certain value?">
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46 <option value="no">No</option>
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47 <option value="yes">Yes</option>
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48 </param>
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49 <when value="no">
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50 <!-- do nothing -->
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51 </when>
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52 <when value="yes">
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53 <param name="factor" type="float" value="0.0" label="Multiply by" />
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54 </when>
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55 </conditional>
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56 <conditional name="reads">
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57 <param name="downstream" type="select" label="Are all reads downstream of the transposon?">
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58 <option value="no">No</option>
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59 <option value="yes">Yes</option>
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60 </param>
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61 <when value="no">
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62 <!-- do nothing -->
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63 </when>
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64 <when value="yes">
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65 <!-- do nothing -->
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66 </when>
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67 </conditional>
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68 </inputs>
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69 <outputs>
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70 <data format="csv" name="output" />
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71 <data format="txt" name="output2" />
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72 <data format="wig" name="output3" />
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73 </outputs>
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74 <help>
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75
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76 **What it does**
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77
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78 This tool consolidates the fitness values of transposon insertion mutations generated by Tn-Seq, and is mostly useful for consolidating values produced by a 4-cycle looping trimming pipeline.
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79
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80 </help>
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81 </tool> |
