annotate EBIsoformMultiCondTest.xml @ 42:66fc1abbdf07 draft

Uploaded
author ning
date Mon, 16 Jun 2014 16:24:23 -0400
parents e11c511a2bb5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
37
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
1 <tool id="EBIsoformMultiCondTest" name="Isoform level DE test across multiple conditions">
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
2 <description>Runs EBSeq to find DE isoforms across multiple (more than two) conditions</description>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
3 <command>R --quiet --slave --file=$GALAXY_ROOT_DIR/tools/EBSeq/EBIsoformMultiCondTest.R --args $Isoform_Expression $First_Row_Sample_Names $Conditions $Ig_Vector $Patterns_of_Interests $PP_of_each_pattern $Pattern_with_highest_PP $Sizes 1>NUL 2>NUL</command>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
4 <inputs>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
5 <param name="Isoform_Expression" type="data" format="tabular" label="Isoform Expression (tab delimited, please use the unnormalized values, e.g. expected counts from RSEM)"/>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
6 <param name="First_Row_Sample_Names" type="select" format="text">
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
7 <label>The First Row is Sample Names?</label>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
8 <option value="y">Yes</option>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
9 <option value="n">No</option>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
10 </param>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
11 <param name="Conditions" type="text" size="60" value="C1,C2,C3" label="Enter which condition each
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
12 sample belongs to (separated by comma, no space please)."
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
13 help=""/>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
14 <param name="Ig_Vector" type="data" format="tabular" label="Ig Vector to define the uncertainty groups"/>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
15 <param name="Patterns_of_Interests" type="data" format="tabular" label="Patterns of Interests"/>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
16 </inputs>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
17 <outputs>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
18 <data format="tabular" name="PP_of_each_pattern" label="PP of each pattern"/>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
19 <data format="tabular" name="Pattern_with_highest_PP" label="Pattern with highest PP"/>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
20 <data format="tabular" name="Sizes" label="Normalization factors"/>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
21 </outputs>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
22
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
23 <help>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
24 The input file and conditions should have more than two levels (for exactly two levels, please use the 'Isoform level DE test across two conditions' tool). Format of the Isoform Expression file should be transcript_id, EC1, EC2 ... Please do not include the gene name in this file. The length of the Condition vector should be exactly the same as the number of columns in the data file (except the isoform names column).
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
25
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
26 The patterns of interests could be obtained by function Get All Possible Patterns (and optionally, if there are too many patterns generated, the function Choose Patterns could be used to choose only subset of the patterns.)
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
27
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
28 The Ig Vector could be generated by the GetIg function or obtained from RSEM output.
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
29
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
30 Three output files will be generated. The first file contains the Posterior probability of being each pattern.
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
31 The second file contains the pattern with the highest PP for each isoform and the normalized expressions. Isoforms are with the same order as in input file.
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
32 The last file provides the library size factor for each sample.
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
33
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
34 </help>
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
35
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
36
e11c511a2bb5 Uploaded
ning
parents:
diff changeset
37 </tool>