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

Uploaded all files tracked by git

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kmersvm/classify.xml	Sun Aug 05 15:32:16 2012 -0400
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+<tool id="kmersvm_classify" name="Score Sequences of Interest">
+  <description>using SVM weights</description>
+  <command interpreter="python">scripts/kmersvm_classify.py -q $inputA $inputB</command>
+  <inputs>
+    <param format="tabular" name="inputA" type="data" label="SVM Weights"/>
+    <param format="fasta" name="inputB" type="data" label="Test Sequences"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="kmersvm_scores.out" from_work_dir="kmersvm_scores.out" />
+  </outputs>
+    <tests>
+        <test>
+                <param name="inputA" value="test_weights.out" />
+                <param name="inputB" value="classify_test.fa" />
+                <output name="output" file="classify_output.out" />
+        </test>
+  </tests>
+  <help>
+
+**What it does**
+
+Takes as input one file of weights generated by Train SVM and one FASTA file containing sequences to be predicted.
+
+Returns a file containing the names of the input sequences, as well as the scores and posterior probabilities of the input sequences.
+
+----
+
+**Example**
+
+Scores file::
+
+    #seq_id	posterior_prob	svm_score
+    mm8_chr1_3089935_3090035_+	0.042414638227	-2.13990367846
+    mm8_chr1_5031335_5031435_+	0.351943600792	-0.478063299876
+    mm8_chr1_5103742_5103842_+	0.194625711202	-1.01493730026
+    mm8_chr1_5650372_5650472_+	0.105376843506	-1.49141463695
+  
+  </help>
+</tool>