Mercurial > repos > iuc > transit_resampling

annotate transit_resampling.xml @ 5:3fcb70c1ca78 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
author iuc
date Mon, 22 Apr 2019 14:40:33 -0400
parents 7288ac4e8583
children 8ab1c8c909a7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
1
1d1ca6b30fbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents: 0
diff changeset
2 <tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy1">
0
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
3 <description>- determine per-gene p-values</description>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
4 <macros>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
5 <import>macros.xml</import>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
6 </macros>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
7 <expand macro="requirements" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
9 @LINK_INPUTS@
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
10 #set $control_files = ','.join(['control_file_%d.wig' % idx for idx, _ in enumerate(str($controls).split(','))])
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
11 #for idx, filename in enumerate(str($controls).split(',')):
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
12 ln -s '$filename' control_file_${idx}.wig &&
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
13 #end for
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
14 transit resampling $input_files $control_files annotation.dat transit_out.txt
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
15 @STANDARD_OPTIONS@
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
16 -s $samples -n $normalization $histogram $adaptive $exclude_zero $pseudo $loess
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
17 ]]>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
18 </command>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
19 <inputs>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
20 <expand macro="standard_inputs">
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
21 <param name="controls" type="data" format="wig" multiple="true" label="Control .wig files" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
22 <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
23 <param name="normalization" argument="-n" type="select" label="Normalization method">
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
24 <option value="TTR">TTR</option>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
25 </param>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
26 <param name="histogram" argument="-h" type="boolean" truevalue="-h" falsevalue="" label="Output histogram of the permutations" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
27 <param name="adaptive" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Perform adaptive resampling" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
28 <param name="exclude_zero" argument="-ez" type="boolean" truevalue="-ez" falsevalue="" label="Exclude rows with zero accross conditions" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
29 <param name="pseudo" argument="-pc" type="boolean" truevalue="-pc" falsevalue="" label="Add pseudocounts at each site" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
30 <param name="loess" argument="-l" type="boolean" truevalue="-l" falsevalue="" label="Perform LOESS Correction" help="Helps remove possible genomic position bias." />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
31
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
32 </expand>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
33 </inputs>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
34 <outputs>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
35 <expand macro="outputs" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
36 </outputs>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
37 <tests>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
38 <test>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
39 <param name="inputs" ftype="wig" value="transit-in1-rep1.wig,transit-in1-rep2.wig" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
40 <param name="controls" ftype="wig" value="transit-co1-rep1.wig,transit-co1-rep2.wig,transit-co1-rep3.wig" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
41 <param name="annotation" ftype="gff3" value="transit-in1.gff3" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
42 <param name="samples" value="1000" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
43 <param name="burnin" value="100" />
4
7288ac4e8583 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit b8111d3ebede6ee71b18fbbabc708cdeab340912-dirty
dave
parents: 3
diff changeset
44 <param name="replicates" value="Replicates" />
0
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
45 <output name="sites" file="resampling-sites1.txt" ftype="tabular" compare="sim_size" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
46 </test>
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
47 </tests>
3
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
48
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
49 <help>
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
50 <![CDATA[.. class:: infomark
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
51
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
52 **What it does**
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
53
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
54 -------------------
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
55
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
56
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
57 The re-sampling method is a comparative analysis the allows that can be used to determine conditional essentiality of genes. It is based on a permutation test, and is capable of determining read-counts that are significantly different across conditions.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
58
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
59 This technique has yet to be formally published in the context of differential essentiality analysis. Briefly, the read-counts at each genes are determined for each replicate of each condition. The total read-counts in condition A is subtracted from the total read counts at condition B, to obtain an observed difference in read counts. The TA sites are then permuted for a given number of “samples”. For each one of these permutations, the difference is read-counts is determined. This forms a null distribution, from which a p-value is calculated for the original, observed difference in read-counts.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
60
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
61
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
62 Note : Can be used for both Himar1 and Tn5 datasets
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
63
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
64
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
65 -------------------
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
66
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
67 **Inputs**
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
68
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
69 -------------------
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
70
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
71 Input files for Resampling need to be:
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
72
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
73 - .wig files : Tabulated files containing one column with the TA site coordinate and one column with the read count at this site.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
74 - annotation .prot_table : Annotation file generated by the `Convert Gff3 to prot_table for TRANSIT` tool.
3
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
75
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
76
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
77 -------------------
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
78
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
79 **Parameters**
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
80
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
81 -------------------
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
82
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
83 Optional Arguments:
3
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
84
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
85 -s <integer> := Number of samples. Default: 10000
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
86 -n <string> := Normalization method. Default: TTR
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
87 -h := Output histogram of the permutations for each gene. Default: Off.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
88 -a := Perform adaptive resampling. Default: Off.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
89 -ez := Exclude rows with zero accross conditions. Default: Off
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
90 --pc := Pseudocounts to be added at each site. Default: 0
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
91 -l := Perform LOESS Correction; Helps remove possible genomic position bias. Default: Off.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
92 --iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: 0.0
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
93 --iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: 0.0
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
94 --ctrl_lib := String of letters representing library of control files in order e.g. 'AABB' Default: empty. Letters used must also be used in --exp_lib. If non-empty, resampling will limit permutations to within-libraries.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
95 --exp_lib := String of letters representing library of experimental files in order e.g. 'ABAB' Default: empty. Letters used must also be used in --ctrl_lib. If non-empty, resampling will limit permutations to within-libraries.
3
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
96
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
97
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
98 The resampling method is non-parametric, and therefore does not require any parameters governing the distributions or the model. The following parameters are available for the method:
3
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
99
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
100 - Samples: The number of samples (permutations) to perform. The larger the number of samples, the more resolution the p-values calculated will have, at the expense of longer computation time. The re-sampling method runs on 10,000 samples by default.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
101 - Output Histograms:Determines whether to output .png images of the histograms obtained from resampling the difference in read-counts.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
102 - Adaptive Resampling: An optional “adaptive” version of resampling which accelerates the calculation by terminating early for genes which are likely not significant. This dramatically speeds up the computation at the cost of less accurate estimates for those genes that terminate early (i.e. deemed not significant). This option is OFF by default.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
103 - Include Zeros: Select to include sites that are zero. This is the preferred behavior, however, unselecting this (thus ignoring sites that) are zero accross all dataset (i.e. completely empty), is useful for decreasing running time (specially for large datasets like Tn5).
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
104 - Normalization Method: Determines which normalization method to use when comparing datasets. Proper normalization is important as it ensures that other sources of variability are not mistakenly treated as real differences. See the Normalization section for a description of normalization method available in TRANSIT.
3
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
105
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
106
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
107 -------------------
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
108
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
109 **Outputs**
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
110
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
111 -------------------
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
112
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
113 The re-sampling method outputs a tab-delimited file with results for each gene in the genome. P-values are adjusted for multiple comparisons using the Benjamini-Hochberg procedure (called “q-values” or “p-adj.”). A typical threshold for conditional essentiality on is q-value < 0.05.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
114
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
115
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
116 ============================================= ========================================================================================================================
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
117 **Column Header** **Column Definition**
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
118 --------------------------------------------- ------------------------------------------------------------------------------------------------------------------------
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
119 Orf Gene ID
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
120 Name Gene Name
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
121 Desc Gene Description
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
122 N Number of TA sites in the gene.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
123 TAs Hit Number of TA sites with at least one insertion.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
124 Sum Rd 1 Sum of read counts in condition 1.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
125 Sum Rd 2 Sum of read counts in condition 2.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
126 Delta Rd Difference in the sum of read counts.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
127 p-value P-value calculated by the permutation test.
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
128 p-adj. Adjusted p-value controlling for the FDR (Benjamini-Hochberg)
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
129 ============================================= ========================================================================================================================
3
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
130
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
131
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
132
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
133 -------------------
3
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
134
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
135 **More Information**
3
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
136
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
137 -------------------
3
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
138
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
139 See `TRANSIT documentation`
3
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
140
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
141 - TRANSIT: https://transit.readthedocs.io/en/latest/index.html
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
142 - `TRANSIT Gumbel`: https://transit.readthedocs.io/en/latest/transit_methods.html#re-sampling
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 4
diff changeset
143 ]]></help>
3
b33af081b02e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 4730eda34222a432a14bf1d1dd090b15e61a494c-dirty
iuc
parents: 1
diff changeset
144
0
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
145 <expand macro="citations" />
8ccb1b841efb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0
iuc
parents:
diff changeset
146 </tool>