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annotate kmersvm/nullseq.xml @ 0:66088269713e draft

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author test-svm
date Sun, 05 Aug 2012 15:32:16 -0400
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1 <tool id="kmersvm_nullseq" name="Generate Null Sequence">
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2 <description>using random sampling from genomic DNA</description>
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3 <command interpreter="python">scripts/nullseq_generate.py -q
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4 #if str($excluded) !="None":
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5 -e $excluded
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6 #end if
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7 -x $fold -r $rseed -g $gc_err -t $rpt_err $input $dbkey ${indices_path.fields.path}
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8 </command>
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9 <inputs>
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10 <param name="fold" type="integer" value="1" label="# of Fold-Increase" />
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11 <param name="gc_err" type="float" value="0.02" label="Allowable GC Error" />
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12 <param name="rpt_err" type="float" value="0.02" label="Allowable Repeat Error" />
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13 <param name="rseed" type="integer" value="1" label="Random Number Seed" />
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14 <param format="interval" name="input" type="data" label="BED File of Positive Regions" />
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15 <validator type="unspecified_build" />
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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." />
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17 <param name="excluded" optional="true" format="interval" type="data" value="None" label="Excluded Regions (optional)" />
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18 <param name="indices_path" type="select" label="Available Datasets">
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19 <options from_file="nullseq_indices.loc">
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20 <column name="dbkey" index="0"/>
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21 <column name="value" index="0"/>
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22 <column name="name" index="1"/>
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23 <column name="path" index="2"/>
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24 <!--filter type="data_meta" ref="input" key="dbkey" column="0" /-->
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25 </options>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data format="interval" name="nullseq_output" from_work_dir="nullseq_output.bed" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input" value="nullseq_test.bed" ftype="bed" />
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34 <param name="fold" value="1" />
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35 <param name="gc_err" value="0.02" />
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36 <param name="rpt_err" value="0'02" />
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37 <param name="rseed" value="1" />
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38 <param name="indices_path" value="hg19" />
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39 <output name="output" file="nullseq_output.bed" />
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40 </test>
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41 </tests>
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42 <help>
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43
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44 **What it does**
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45
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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.
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47
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48 **Parameters**
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49
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50 Fold-Increase: Size of desired null sequence data set expressed as multiple of the size of the input data set.
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51
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52 GC Error, Repeat Error: Acceptable difference between a positive sequence and its corresponding null sequence in terms of GC content, repeat content.
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53
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54 Random Number Seed: Seed for random number generator.
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55
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56 Excluded Regions: Submitted regions will be excluded from null sequence generation.
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57
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58 ----
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59
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60 **Example**
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61
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62 Given a BED file containing::
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63
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64 chr1 10212203 10212303
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65 chr1 103584748 103584848
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66 chr1 105299130 105299230
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67 chr1 106367772 106367872
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68
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69 Tool will output BED file matched in length, GC content and repeat content::
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71 chr1 3089935 3090035
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72 chr1 5031335 5031435
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73 chr1 5103742 5103842
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74 chr1 5650372 5650472
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75
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76 </help>
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77 </tool>