diff overlapselect_wrapper.xml @ 0:84f5e02c76f3 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/overlapselect_wrapper.xml	Wed May 21 03:30:16 2014 -0400
@@ -0,0 +1,147 @@
+<tool id="overlapselect_wrapper" name="overlap Select" version="1.0">
+     <requirements>
+       <requirement type='package' version="latest">overlapSelect</requirement>
+     </requirements>
+
+
+  <description>UCSC Overlap Select</description>
+  <command interpreter="bash">
+	overlapselect_wrapper.sh
+#if $optionSpec.parType == "specify":
+    #if $str($optionSpec.strand) == "true":
+        -strand
+    #end if
+    #if $str($optionSpec.oppositeStrand) == "true":
+        -oppositeStrand
+    #end if
+    #if $str($optionSpec.nonOverlapping) == "true":
+        -nonOverlapping
+    #end if
+    #if $str($optionSpec.mergeOutput) == "true":
+        -mergeOutput
+    #end if
+    -overlapBases=$optionSpec.overlapBases
+    -overlapThreshold=$optionSpec.overlapThreshold
+    -overlapThresholdCeil=$optionSpec.overlapThresholdCeil
+    #if $str($optionSpec.selectFormat) == "bed":
+        -selectFmt=bed
+    #end if
+    #if $str($optionSpec.inFormat) == "bed":
+        -inFmt=bed
+    #end if
+    #if $str($optionSpec.selectFormat) == "tab":
+        -selectCoordCols=$optionSpec.selColStart
+    #end if
+    #if $str($optionSpec.inFormat) == "tab":
+        -inCoordCols=$optionSpec.inColStart
+    #end if
+#else
+    -selectFmt=bed inFmt=bed
+#end if
+    $selectFile
+    $inFile
+    $outFile
+  </command>
+  <inputs>
+    <param name="inFile" type="data" format="Tabular" metadata_name="dbkey" label="Select the query (input) file" />
+    <param name="selectFile" type="data" format="Tabular" metadata_name="dbkey" label="Select the reference (select) file" />
+    <conditional name="optionSpec">      
+      <param name="parType" type="select" label="Do you want to select your target from the list or from your history?" help="">
+        <option value="default">Use Default Parameters</option>
+        <option value="specify">Specify Parameters</option>
+      </param>
+      <when value="default">
+      </when>
+      <when value="specify">
+        <param name="selectFormat" type="select" label="Query File Format -selectFmt">
+                          <option value="bed">Bed</option>
+                          <option value="tab">Tabular</option>
+        </param>
+        <param name="inFormat" type="select" label="Reference File Format -inFmt">
+                          <option value="bed">Bed</option>
+                          <option value="tab">Tabular</option>
+        </param>
+        <param name="selColStart" type="integer" value="0" label="Query File is unstranded with chr starting at this column (0 based - i.e. 0=col1), followed by start and end (-1 to disable)-selectCoordCols" /> 
+        <param name="inColStart" type="integer" value="0" label="Reference File is unstranded with chr starting at this column (0 based - i.e. 0=col1), followed by start and end  (-1 to disable)-inCoordCols" /> 
+        <param name="strand" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only search on same strand -strand" />
+        <param name="oppositeStrand" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only search on opposite strand -oppositeStrand" />
+        <param name="nonOverlapping" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Select non-overlapping instead of overlapping records" />
+        <param name="mergeOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge Output -mergeOutput" />
+        <param name="overlapBases" type="integer" value="-1" label="Number of overlap minimum (-overlapBases) (-1 to disable)" /> 
+        <param name="overlapThreshold" type="float" value="0.0" label="Minimum fraction overlap" help="minimum fraction of an inFile record that must be overlapped by a single select record to be considered
+        overlapping.  Note that this is only coverage by a single select record, not total coverage" /> 
+        <param name="overlapThresholdCeil" type="float" value="1.1" label="Maximum fraction overlap" help="select only inFile records with less than this amount of overlap with a single record, provided they are selected by other criteria." /> 
+
+      </when>  <!-- history -->	  	  
+    </conditional>  <!-- optionSpec -->
+  </inputs>
+  <outputs>
+    <data format="interval" name="outFile" label="Overlapselect on ${selectFile.name} vs ${inFile.name} "/>
+  </outputs>
+  <tests>
+  	<test>
+		<param name="inFile" value="NM_001206.gp"/>
+		<param name="selectFile" value="mrna.psl"/>
+		<output name="outFile" value="psl_over_NM_001206gp.psl"/>
+  	</test>
+  </tests>
+  
+<help>
+**Overlap Select Help**
+
+
+**Options**
+
+* selectCds - Use only CDS in the selectFile
+
+* selectRange - Use entire range instead of blocks from records in the selectFile.
+
+* inFmt=fmt - specify inFile format, same values as -selectFmt.
+
+* inCoordCols=spec - inFile is tab-separate with coordinates specified by spec, in format described above.
+
+* inCds - Use only CDS in the inFile
+
+* inRange - Use entire range instead of blocks of records in the inFile.
+
+* nonOverlapping - select non-overlapping instead of overlapping records
+
+* strand - must be on the same strand to be considered overlapping
+
+* oppositeStrand - must be on the opposite strand to be considered overlapping
+
+* excludeSelf - don't compare records with the same coordinates and name. Warning: using only one of -inCds or -selectCds will result in different coordinates for the same record.
+
+* idMatch - only select overlapping records if they have the same id
+
+* aggregate - instead of computing overlap bases on individual select entries, compute it based on the total number of inFile bases overlap by selectFile records. -overlapSimilarity and -mergeOutput will not work with this option.
+
+* overlapThreshold=0.0 - minimum fraction of an inFile record that must be overlapped by a single select record to be considered overlapping.  Note that this is only coverage by a single select record, not total coverage.
+
+* overlapThresholdCeil=1.1 - select only inFile records with less than this amount of overlap with a single record, provided they are selected by other criteria.
+
+* overlapSimilarity=0.0 - minimum fraction of inFile and select records that: Note that this is only coverage by a single select record and this  is; bidirectional inFile and selectFile must overlap by this amount.  A value of 1.0 will select identical records (or CDS if  both CDS options are specified.  Not currently supported with  *aggregate.*
+
+* overlapSimilarityCeil=1.1 - select only inFile records with less than this amount of similarity with a single record. provided they are selected by other criteria.
+
+* overlapBases=-1 - minimum number of bases of overlap, lt 0 disables.
+
+* statsOutput - output overlap statistics instead of selected records. If no overlap criteria is specified, all overlapping entries are reported, Otherwise only the pairs passing the criteria are reported. This results in a tab-separated file with the columns:  inId selectId inOverlap selectOverlap overBases: Where inOverlap is the fraction of the inFile record overlapped by the selectFile record and selectOverlap is the fraction of the select record overlap by inFile records.  With -aggregate, output is: inId inOverlap inOverBases inBases 
+
+* statsOutputAll - like -statsOutput, however output all inFile records, including those that are not overlapped.
+
+* statsOutputBoth - like -statsOutput, however output all selectFile and inFile records, including those that are not overlapped.
+
+* mergeOutput - output file with be a merge of the input file with the selectFile records that selected it.  The format is inRec selectRec. if multiple select records hit, inRec is repeated. This will increase
+      the memory required. Not supported with -nonOverlapping or -aggregate.
+      
+* idOutput - output a tab-separated file of pairs of inId selectId with -aggregate, only a single column of inId is written
+
+* dropped=file  - output rows that were dropped to this file.
+
+* verbose=n - verbose gt 1 prints some details,
+
+
+  </help>
+</tool>
+