annotate consol_fit.xml @ 1:c5d9dd4b6a5a draft

Uploaded
author kaymccoy
date Thu, 11 Aug 2016 18:07:39 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
1 <tool id="consolidate_fitnesses" name="Consolidate Fitnesses">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
2 <description>of transposon insertion locations</description>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
3 <requirements>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
4 <requirement type="package" version="1.64">biopython</requirement>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
5 </requirements>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
6 <command interpreter="python">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
7 consol_fit.py
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
8 -i $input
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
9 -calctxt $calctxt
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
10 -out $output
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
11 -out2 $output2
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
12 -maxweight $maxweight
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
13 -cutoff $cutoff
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
14 -cutoff2 $cutoff2
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
15 -wig $output3
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
16 #if $normalization.calculations == "yes":
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
17 -normalize $normalization.genes
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
18 #end if
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
19 #if $multiply.choice == "yes":
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
20 -multiply $multiply.factor
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
21 #end if
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
22 #if $reads.downstream == "yes":
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
23 -d 1
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
24 #end if
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
25 </command>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
26 <inputs>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
27 <param name="input" type="data" label="Fitness file"/>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
28 <param name="calctxt" type="data" label="the txt file output from calc_fitness"/>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
29 <conditional name="normalization">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
30 <param name="calculations" type="select" label="Normalize fitness calculations?">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
31 <option value="no">No</option>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
32 <option value="yes">Yes</option>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
33 </param>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
34 <when value="no">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
35 <!-- do nothing -->
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
36 </when>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
37 <when value="yes">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
38 <param name="genes" type="data" label="Genes to normalize by" />
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
39 </when>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
40 </conditional>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
41 <param name="cutoff" type="float" value="0.0" label="Cutoff"/>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
42 <param name="cutoff2" type="float" value="0.0" label="Cutoff2"/>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
43 <param name="maxweight" type="float" value="75" label="Maximum weight of a transposon gene in normalization calculations"/>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
44 <conditional name="multiply">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
45 <param name="choice" type="select" label="Multiply fitness scores by a certain value?">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
46 <option value="no">No</option>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
47 <option value="yes">Yes</option>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
48 </param>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
49 <when value="no">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
50 <!-- do nothing -->
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
51 </when>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
52 <when value="yes">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
53 <param name="factor" type="float" value="0.0" label="Multiply by" />
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
54 </when>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
55 </conditional>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
56 <conditional name="reads">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
57 <param name="downstream" type="select" label="Are all reads downstream of the transposon?">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
58 <option value="no">No</option>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
59 <option value="yes">Yes</option>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
60 </param>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
61 <when value="no">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
62 <!-- do nothing -->
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
63 </when>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
64 <when value="yes">
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
65 <!-- do nothing -->
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
66 </when>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
67 </conditional>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
68 </inputs>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
69 <outputs>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
70 <data format="csv" name="output" />
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
71 <data format="txt" name="output2" />
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
72 <data format="wig" name="output3" />
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
73 </outputs>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
74 <help>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
75
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
76 **What it does**
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
77
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
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.
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
79
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
80 </help>
c5d9dd4b6a5a Uploaded
kaymccoy
parents:
diff changeset
81 </tool>