annotate compGenes.xml @ 4:0cf314cf3186 draft

Uploaded
author antmarge
date Wed, 29 Mar 2017 14:39:36 -0400
parents 5ff933ea9878
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
1 <tool id="compGenes" name="Compare Genes" version="0.1.0">
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
2
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
3 <!-- Margaret Antonio 17.01.08 -->
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
4
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
5 <description> compare gene aggregate fitness from two different experiments</description>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
6
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
7 <requirements>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
8 <requirement type="package" version="5.18.1">perl</requirement>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
9 <requirement type="package" version="2.45">perl_getopt_long</requirement>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
10 <requirement type="package" version="1.02">perl_statistics_distributions</requiremnt>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
11 </requirements>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
12
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
13 <command interpreter="perl">
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
14 compGenes.pl
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
15 -input1 $input1
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
16 -input2 $input2
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
17 -l1 $l1
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
18 -l2 $l2
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
19 -o $outfile
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
20 </command>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
21
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
22 <inputs>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
23 <param name="input1" type="data" label="csv gene aggregate fitness file #1"/>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
24 <param name="input2" type="data" label="csv gene aggregate fitness file #2"/>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
25 <param name="l1" type="text" value ="input1" label="Label for input #1"/>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
26 <param name="l2" type="text" value ="input2" label="Label for input #2"/>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
27
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
28
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
29 </inputs>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
30
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
31 <outputs>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
32 <data format="csv" name="outfile" />
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
33 </outputs>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
34
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
35 <help>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
36 **What it does**
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
37
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
38 This tool compares genes for an organism under different conditions. It takes two geneAgregate outputs and compares them calculating the difference in mean fitness for each gene. Example usage: compare organism in presence of control vs antibiotic. For different strains/genomes, where gene ids are not the same, use compStrains.pl;
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
39
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
40
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
41 **The options explained**
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
42
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
43 Input 1 and 2: These are the csv (comma separated values) files containing the gene fitness values. Since they should have been produced by the "Aggregate Fitness" tool, each line besides the header should represent the following information for a gene: Locus, Fitness, NumberofInsertions, StandardDev of insertion fitness, Standard Error of insertion fitness, and Marking
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
44
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
45 Label 1 and 2: Labels for the column headers for files in the comparison
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
46
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
47
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
48 The name of your output file: self-explanatory. Remember to have it end in ".csv".
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
49
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
50
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
51 </help>
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
52
5ff933ea9878 Uploaded
antmarge
parents:
diff changeset
53 </tool>