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author kaymccoy
date Fri, 12 Aug 2016 16:44:38 -0400
parents c5d9dd4b6a5a
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7:4b2fc35b32b0 8:b108f7fe9493
1 <tool id="consolidate_fitnesses" name="Consolidate Fitnesses">
2 <description>of transposon insertion locations</description>
3 <requirements>
4 <requirement type="package" version="1.64">biopython</requirement>
5 </requirements>
6 <command interpreter="python">
7 consol_fit.py
8 -i $input
9 -calctxt $calctxt
10 -out $output
11 -out2 $output2
12 -maxweight $maxweight
13 -cutoff $cutoff
14 -cutoff2 $cutoff2
15 -wig $output3
16 #if $normalization.calculations == "yes":
17 -normalize $normalization.genes
18 #end if
19 #if $multiply.choice == "yes":
20 -multiply $multiply.factor
21 #end if
22 #if $reads.downstream == "yes":
23 -d 1
24 #end if
25 </command>
26 <inputs>
27 <param name="input" type="data" label="Fitness file"/>
28 <param name="calctxt" type="data" label="the txt file output from calc_fitness"/>
29 <conditional name="normalization">
30 <param name="calculations" type="select" label="Normalize fitness calculations?">
31 <option value="no">No</option>
32 <option value="yes">Yes</option>
33 </param>
34 <when value="no">
35 <!-- do nothing -->
36 </when>
37 <when value="yes">
38 <param name="genes" type="data" label="Genes to normalize by" />
39 </when>
40 </conditional>
41 <param name="cutoff" type="float" value="0.0" label="Cutoff"/>
42 <param name="cutoff2" type="float" value="0.0" label="Cutoff2"/>
43 <param name="maxweight" type="float" value="75" label="Maximum weight of a transposon gene in normalization calculations"/>
44 <conditional name="multiply">
45 <param name="choice" type="select" label="Multiply fitness scores by a certain value?">
46 <option value="no">No</option>
47 <option value="yes">Yes</option>
48 </param>
49 <when value="no">
50 <!-- do nothing -->
51 </when>
52 <when value="yes">
53 <param name="factor" type="float" value="0.0" label="Multiply by" />
54 </when>
55 </conditional>
56 <conditional name="reads">
57 <param name="downstream" type="select" label="Are all reads downstream of the transposon?">
58 <option value="no">No</option>
59 <option value="yes">Yes</option>
60 </param>
61 <when value="no">
62 <!-- do nothing -->
63 </when>
64 <when value="yes">
65 <!-- do nothing -->
66 </when>
67 </conditional>
68 </inputs>
69 <outputs>
70 <data format="csv" name="output" />
71 <data format="txt" name="output2" />
72 <data format="wig" name="output3" />
73 </outputs>
74 <help>
75
76 **What it does**
77
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.
79
80 </help>
81 </tool>