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

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

<tool id="kmersvm_nullseq" name="Generate Null Sequence">
  <description>using random sampling from genomic DNA</description>
  <command interpreter="python">scripts/nullseq_generate.py -q 
  	#if str($excluded) !="None":
  		-e $excluded
  	#end if
  	-x $fold -r $rseed -g $gc_err -t $rpt_err $input $dbkey ${indices_path.fields.path}
  </command>
  <inputs>
    <param name="fold" type="integer" value="10" label="# of Fold-Increase" min="1" max="50" />
    <param name="gc_err" type="float" value="0.02" label="Allowable GC Error" min="0.01" max="0.1"/>
    <param name="rpt_err" type="float" value="0.02" label="Allowable Repeat Error" min="0.01" max="0.1"/>
    <param name="rseed" type="integer" value="1" label="Random Number Seed" />    
    <param format="interval" name="input" type="data" label="BED File of Positive Regions" />
      <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="excluded" optional="true" format="interval" type="data" value="None" label="Excluded Regions (optional)" />  
    <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="interval" name="nullseq_output" from_work_dir="nullseq_output.bed" />
  </outputs>
  <tests>
	  <test>
		  <param name="input" value="nullseq_test.bed" />
		  <param name="fold" value="1" />
		  <param name="gc_err" value="0.02" />
		  <param name="rpt_err" value="0.02" />
		  <param name="rseed" value="1" />
		  <param name="indices_path" value="hg19" />
		  <output name="output" file="nullseq_output.bed" />
	  </test>
  </tests>
  <help>
  
**What it does**
  
Takes an input BED file and generates a set of sequences for use as negative data (null sequences) in Train SVM similar in length, GC content and repeat fraction.  Uses random sampling for efficiency.

----

**Recommended Settings**

Fold-Increase: Default is recommended, up to 50x positive set.

GC Error, Repeat Error: Default is recommended.

----
  
**Parameters**
  
Fold-Increase: Size of desired null sequence data set expressed as multiple of the size of the input data set.
  
GC Error, Repeat Error: Acceptable difference between a positive sequence and its corresponding null sequence in terms of GC content, repeat content.
  
Random Number Seed:  Seed for random number generator.

Excluded Regions:  Submitted regions will be excluded from null sequence generation.

----
  
**Example**
  
Given a BED file containing::
  
    chr1	10212203	10212303
    chr1	103584748	103584848
    chr1	105299130	105299230
    chr1	106367772	106367872
	
Tool will output BED file matched in length, GC content and repeat content::
  
    chr1	3089935	3090035
    chr1	5031335	5031435
    chr1	5103742	5103842
    chr1	5650372	5650472
	
  </help>
</tool>