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

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

<tool id="kmersvm_seqprofile" name="Sequence Profiles">
  <description>provide length, gc content, and repeat fraction of each sequence</description>
  <command interpreter="python">scripts/make_profile.py $input $dbkey ${indices_path.fields.path} seq_profile.txt</command>
  <inputs>
	<param format="interval" name="input" type="data" label="BED File of Regions of interest" />
      <validator type="unspecified_build" />
      <validator type="dataset_metadata_in_file" filename="nullseq_indices.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are currently unavailable for the specified build." />
    <param name="indices_path" type="select" label="Available Datasets">
      <options from_file="nullseq_indices.loc">
        <column name="dbkey" index="0"/>
        <column name="value" index="0"/>
        <column name="name" index="1"/>
        <column name="path" index="2"/>
        <filter type="data_meta" ref="input" key="dbkey" column="0" /> 
      </options>
    </param>
  </inputs>
  <outputs>
	  <data format="tabular" name="seq_profile.txt" from_work_dir="seq_profile.txt" />
  </outputs>
  <help>

**What it does**

Takes as input a BED file and the file's corresponding genome build.

Returns length, GC and repeat content information for each interval in bed file.

----

**Example**

Profile file::

	mm9_chr10_6238300_6238926_+	626	0.525559105431	0.0
	mm9_chr10_7757450_7758801_+	1351	0.451517394523	0.0384900074019
	mm9_chr10_8992150_8992551_+	401	0.411471321696	0.0
	mm9_chr10_9265550_9266026_+	476	0.38025210084	0.0
	
  </help>
</tool>