annotate compStrains.xml @ 17:bc81db58983c draft

Uploaded
author antmarge
date Wed, 29 Mar 2017 14:21:12 -0400
parents 02d7230ec559
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
1 <tool id="compStrains" name="Compare Strains" version="0.1.0">
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
2
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
3 <!-- Margaret Antonio 17.01.08 -->
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
4
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
5 <description> compare gene aggregate fitness from two different experiments for two different strains (genomes)</description>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
6
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
7 <requirements>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
8 <requirement type="package" version="5.18.1">perl</requirement>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
9 <requirement type="package" version="2.45">perl_getopt_long</requirement>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
10 <requirement type="package" version="1.02">perl_statistics_distributions</requirement>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
11 <requirement type="package" version="2.121">perl_data_dumper</requirement>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
12 <requirement type="package" version="2.12">perl_file_path</requirement>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
13 <requirement type="package" version="5.24.1">perl_file_basename</requirement>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
14 </requirements>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
15
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
16 <command interpreter="perl">
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
17 compStrains.pl
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
18 -input1 $input1
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
19 -input2 $input2
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
20 -c $cfile
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
21 -l1 $l1
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
22 -l2 $l2
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
23 -o $outfile
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
24 </command>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
25
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
26 <inputs>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
27 <param name="input1" type="data" label="csv gene aggregate fitness file #1"/>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
28 <param name="input2" type="data" label="csv gene aggregate fitness file #2"/>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
29 <param name="l1" type="text" value ="input1" label="Label for input #1"/>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
30 <param name="l2" type="text" value ="input2" label="Label for input #2"/>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
31 <param name="cfile" type="data" label="Conversion file for homologous genes"/>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
32
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
33
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
34 </inputs>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
35
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
36 <outputs>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
37 <data format="csv" name="outfile" />
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
38 </outputs>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
39
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
40 <help>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
41 **What it does**
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
42
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
43 This tool compares genes for different strains under a single condition. It takes two geneAgregate outputs and compares them calculating the difference in mean fitness for each gene. A tab-delimited conversion file, with one set of gene homologs per line is required Example usage: compare two strains of in presence of an antibiotic. For the same strain/genome, where gene ids are the same, use compGenes.pl;
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
44
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
45
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
46 **The options explained**
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
47
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
48 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
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
49
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
50 Label 1 and 2: Labels for the column headers for files in the comparison
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
51
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
52 Conversion File: Tab-delimited file of homologous genes for the two strains. One set of homologs per line, with each gene id separated by a tab.
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
53
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
54
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
55
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
56 </help>
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
57
02d7230ec559 Uploaded
antmarge
parents:
diff changeset
58 </tool>