view kmersvm/classify.xml @ 7:fd740d515502 draft default tip

Uploaded revised kmer-SVM to include modules from kmer-visual.

<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>