Mercurial > repos > test-svm > kmersvm_test

annotate kmersvm/classify.xml @ 0:66088269713e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded all files tracked by git
author test-svm
date Sun, 05 Aug 2012 15:32:16 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
1 <tool id="kmersvm_classify" name="Score Sequences of Interest">
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
2 <description>using SVM weights</description>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
3 <command interpreter="python">scripts/kmersvm_classify.py -q $inputA $inputB</command>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
4 <inputs>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
5 <param format="tabular" name="inputA" type="data" label="SVM Weights"/>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
6 <param format="fasta" name="inputB" type="data" label="Test Sequences"/>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
7 </inputs>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
8 <outputs>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
9 <data format="tabular" name="kmersvm_scores.out" from_work_dir="kmersvm_scores.out" />
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
10 </outputs>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
11 <tests>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
12 <test>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
13 <param name="inputA" value="test_weights.out" />
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
14 <param name="inputB" value="classify_test.fa" />
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
15 <output name="output" file="classify_output.out" />
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
16 </test>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
17 </tests>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
18 <help>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
19
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
20 **What it does**
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
21
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
22 Takes as input one file of weights generated by Train SVM and one FASTA file containing sequences to be predicted.
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
23
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
24 Returns a file containing the names of the input sequences, as well as the scores and posterior probabilities of the input sequences.
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
25
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
26 ----
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
27
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
28 **Example**
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
29
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
30 Scores file::
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
31
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
32 #seq_id posterior_prob svm_score
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
33 mm8_chr1_3089935_3090035_+ 0.042414638227 -2.13990367846
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
34 mm8_chr1_5031335_5031435_+ 0.351943600792 -0.478063299876
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
35 mm8_chr1_5103742_5103842_+ 0.194625711202 -1.01493730026
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
36 mm8_chr1_5650372_5650472_+ 0.105376843506 -1.49141463695
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
37
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
38 </help>
66088269713e Uploaded all files tracked by git
test-svm
parents:
diff changeset
39 </tool>