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

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Uploaded revised kmer-SVM to include modules from kmer-visual.
author cafletezbrant
date Sun, 16 Jun 2013 18:06:14 -0400
parents 7fe1103032f7
children
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6:1aea7c1a9ab1 7:fd740d515502
5 -e $excluded 5 -e $excluded
6 #end if 6 #end if
7 -x $fold -r $rseed -g $gc_err -t $rpt_err $input $dbkey ${indices_path.fields.path} 7 -x $fold -r $rseed -g $gc_err -t $rpt_err $input $dbkey ${indices_path.fields.path}
8 </command> 8 </command>
9 <inputs> 9 <inputs>
10 <param name="fold" type="integer" value="1" label="# of Fold-Increase" /> 10 <param name="fold" type="integer" value="10" label="# of Fold-Increase" min="1" max="50" />
11 <param name="gc_err" type="float" value="0.02" label="Allowable GC Error" /> 11 <param name="gc_err" type="float" value="0.02" label="Allowable GC Error" min="0.01" max="0.1"/>
12 <param name="rpt_err" type="float" value="0.02" label="Allowable Repeat Error" /> 12 <param name="rpt_err" type="float" value="0.02" label="Allowable Repeat Error" min="0.01" max="0.1"/>
13 <param name="rseed" type="integer" value="1" label="Random Number Seed" /> 13 <param name="rseed" type="integer" value="1" label="Random Number Seed" />
14 <param format="interval" name="input" type="data" label="BED File of Positive Regions" /> 14 <param format="interval" name="input" type="data" label="BED File of Positive Regions" />
15 <validator type="unspecified_build" /> 15 <validator type="unspecified_build" />
16 <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." /> 16 <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." />
17 <param name="excluded" optional="true" format="interval" type="data" value="None" label="Excluded Regions (optional)" /> 17 <param name="excluded" optional="true" format="interval" type="data" value="None" label="Excluded Regions (optional)" />
42 <help> 42 <help>
43 43
44 **What it does** 44 **What it does**
45 45
46 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. 46 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.
47
48 ----
49
50 **Recommended Settings**
51
52 Fold-Increase: Default is recommended, up to 50x positive set.
53
54 GC Error, Repeat Error: Default is recommended.
55
56 ----
47 57
48 **Parameters** 58 **Parameters**
49 59
50 Fold-Increase: Size of desired null sequence data set expressed as multiple of the size of the input data set. 60 Fold-Increase: Size of desired null sequence data set expressed as multiple of the size of the input data set.
51 61