annotate dataOverview.xml @ 2:3ed885628c9f draft

Uploaded
author antmarge
date Tue, 28 Mar 2017 21:56:19 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
1 <tool id="dataOverview" name="Data Overview" version="0.1.0">
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
2
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
3 <!-- Margaret Antonio 17.01.08 -->
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
4
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
5 <description>summarize Tn-Seq libraries and genome</description>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
6
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
7 <requirements>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
8 <requirement type="package" version="5.18.1">perl</requirement>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
9 <requirement type="package" version="2.45">perl_getopt_long</requirement>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
10 <requirement type="package" version="1.6.922">bioperl</requirement>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
11 </requirements>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
12
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
13 <command interpreter="perl">
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
14 dataOverview.pl
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
15 -f $fastaFile
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
16 -r $ref
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
17 -w $weight_ceiling
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
18 -c $cutoff
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
19 -o $outfile
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
20 $input
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
21 #for $a in $additionalcsv
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
22 ${a.input2}
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
23 #end for
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
24 </command>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
25
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
26 <inputs>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
27 <param name="input" type="data" label="csv fitness file"/>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
28 <repeat name="additionalcsv" title="Additional csv fitness file(s)">
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
29 <param name="input2" type="data" label="Select" />
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
30 </repeat>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
31 <param format="fasta" name="fastaFile" type="data" label="Fasta file"/>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
32 <param name="ref" type="data" label="GenBank reference genome"/>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
33 <param name="cutoff" type="integer" value="10" label="Cutoff"/>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
34 <param name="weight_ceiling" type="integer" value="50" label="Weight ceiling"/>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
35
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
36
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
37 </inputs>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
38
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
39 <outputs>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
40 <data format="txt" name="outfile" />
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
41 </outputs>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
42
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
43 <help>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
44 **What it does**
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
45
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
46 This tool summarizes the Tn-Seq single insertion libraries and the organism's genome.
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
47
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
48 **The options explained**
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
49
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
50 The csv fitness file(s): These are the csv (comma separated values) files containing the fitness values that will be used in downstream analyses. Since they should have been produced by the "Calculate Fitness" tool, each line besides the header should represent the following information for an insertion location: position,strand,count_1,count_2,ratio,mt_freq_t1,mt_freq_t2,pop_freq_t1,pop_freq_t2,gene,D,W,nW
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
51
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
52 GenBank reference genome: the reference genome of whatever model you're working with, which needs to be in standard genbank format. For more on that format see the genbank website.
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
53
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
54 Weight ceiling: This value lets you set a weight ceiling for the weights of fitness values. It's only relevant if you're using weighted algorithms.
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
55
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
56 Cutoff: This value lets you ignore the fitness scores of any insertion locations with an average count (the number of counts from t1 and t2 divided by 2) less than it.
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
57
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
58 The name of your output file: self-explanatory. Remember to have it end in ".csv".
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
59
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
60
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
61 </help>
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
62
3ed885628c9f Uploaded
antmarge
parents:
diff changeset
63 </tool>