Repository 's_mart'
hg clone https://toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart

Changeset 56:97aa2e42bfdf (2014-02-05)
Previous changeset 55:2ac71607aa60 (2014-01-10) Next changeset 57:36eaa579fdb6 (2014-02-07)
Commit message:
Uploaded
modified:
SMART/Java/Python/cleaning/GffCleaner.py
SMART/Java/Python/cleaning/GtfCleaner.py
SMART/galaxy/Clusterize.xml
SMART/galaxy/CollapseReads.xml
SMART/galaxy/CompareOverlappingSmallQuery.xml
SMART/galaxy/CompareOverlappingSmallRef.xml
SMART/galaxy/ConvertTranscriptFile.xml
added:
SMART/Java/Python/__init__.pyc
SMART/Java/Python/cleaning/CleanerChooser.pyc
SMART/Java/Python/cleaning/DefaultCleaner.pyc
SMART/Java/Python/cleaning/GffCleaner.pyc
SMART/Java/Python/cleaning/GtfCleaner.pyc
SMART/Java/Python/cleaning/TranscriptListCleaner.pyc
SMART/Java/Python/cleaning/__init__.pyc
SMART/Java/Python/misc/Progress.pyc
SMART/Java/Python/misc/UnlimitedProgress.pyc
SMART/Java/Python/misc/Utils.pyc
SMART/Java/Python/misc/__init__.pyc
SMART/Java/Python/mySql/MySqlTable.pyc
SMART/Java/Python/mySql/__init__.pyc
SMART/Java/Python/ncList/FileSorter.pyc
SMART/Java/Python/ncList/NCIndex.pyc
SMART/Java/Python/ncList/NCList.pyc
SMART/Java/Python/ncList/NCListCursor.pyc
SMART/Java/Python/ncList/NCListFilePickle.pyc
SMART/Java/Python/ncList/__init__.pyc
SMART/Java/Python/structure/Bins.pyc
SMART/Java/Python/structure/Interval.pyc
SMART/Java/Python/structure/Mapping.pyc
SMART/Java/Python/structure/Sequence.pyc
SMART/Java/Python/structure/SequenceList.pyc
SMART/Java/Python/structure/SubMapping.pyc
SMART/Java/Python/structure/Transcript.pyc
SMART/Java/Python/structure/TranscriptList.pyc
SMART/Java/Python/structure/__init__.pyc
SMART/Java/__init__.pyc
SMART/__init__.pyc
SMART/galaxy/removeIntrons.xml
commons/__init__.pyc
commons/core/__init__.pyc
commons/core/checker/RepetException.pyc
commons/core/checker/__init__.pyc
commons/core/coord/Align.pyc
commons/core/coord/Map.pyc
commons/core/coord/Range.pyc
commons/core/coord/__init__.pyc
commons/core/parsing/AxtParser.pyc
commons/core/parsing/BamParser.pyc
commons/core/parsing/BedParser.pyc
commons/core/parsing/BlastParser.pyc
commons/core/parsing/BowtieParser.pyc
commons/core/parsing/CoordsParser.pyc
commons/core/parsing/ElandParser.pyc
commons/core/parsing/ExoParser.pyc
commons/core/parsing/FastaParser.pyc
commons/core/parsing/FastqParser.pyc
commons/core/parsing/GffParser.pyc
commons/core/parsing/GtfParser.pyc
commons/core/parsing/MapParser.pyc
commons/core/parsing/MapperParser.pyc
commons/core/parsing/MaqParser.pyc
commons/core/parsing/NCListParser.pyc
commons/core/parsing/ParserChooser.pyc
commons/core/parsing/PklParser.pyc
commons/core/parsing/PslParser.pyc
commons/core/parsing/RmapParser.pyc
commons/core/parsing/SamParser.pyc
commons/core/parsing/SeqmapParser.pyc
commons/core/parsing/SequenceListParser.pyc
commons/core/parsing/ShrimpParser.pyc
commons/core/parsing/Soap2Parser.pyc
commons/core/parsing/SoapParser.pyc
commons/core/parsing/TranscriptListParser.pyc
commons/core/parsing/WigParser.pyc
commons/core/parsing/__init__.pyc
commons/core/seq/Bioseq.pyc
commons/core/seq/__init__.pyc
commons/core/writer/BedWriter.pyc
commons/core/writer/CsvWriter.pyc
commons/core/writer/EmblWriter.pyc
commons/core/writer/FastaWriter.pyc
commons/core/writer/FastqWriter.pyc
commons/core/writer/GbWriter.pyc
commons/core/writer/Gff2Writer.pyc
commons/core/writer/Gff3Writer.pyc
commons/core/writer/GtfWriter.pyc
commons/core/writer/MapWriter.pyc
commons/core/writer/SamWriter.pyc
commons/core/writer/SequenceListWriter.pyc
commons/core/writer/TranscriptListWriter.pyc
commons/core/writer/UcscWriter.pyc
commons/core/writer/WigWriter.pyc
commons/core/writer/WriterChooser.pyc
commons/core/writer/__init__.pyc
removed:
SMART/galaxy/removeExonLines.xml
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/__init__.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/CleanerChooser.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/DefaultCleaner.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/GffCleaner.py
--- a/SMART/Java/Python/cleaning/GffCleaner.py Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/Java/Python/cleaning/GffCleaner.py Wed Feb 05 11:51:11 2014 -0500
[
@@ -123,7 +123,7 @@
  def parse(self):
  progress = UnlimitedProgress(100000, "Reading input file", self.verbosity)
  for cpt, line in enumerate(self.inputHandle):
- if not line or line[0] == "#": continue
+ if not line or (not line.strip()) or line[0] == "#": continue
  if line[0] == ">": break
  parsedLine = ParsedLine(line, cpt)
  if self.acceptedTypes == None or parsedLine.type in self.acceptedTypes:
b
diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/GffCleaner.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/GtfCleaner.py
--- a/SMART/Java/Python/cleaning/GtfCleaner.py Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/Java/Python/cleaning/GtfCleaner.py Wed Feb 05 11:51:11 2014 -0500
[
@@ -96,7 +96,7 @@
  def parse(self):
  progress = UnlimitedProgress(100000, "Reading input file", self.verbosity)
  for cpt, line in enumerate(self.inputHandle):
- if not line or line[0] == "#": continue
+ if not line or (not line.strip()) or line[0] == "#": continue
  parsedLine = ParsedLine(line, cpt)
  if self.acceptedTypes == None or parsedLine.type in self.acceptedTypes:
  transcriptId = parsedLine.transcriptId
b
diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/GtfCleaner.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/TranscriptListCleaner.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/cleaning/__init__.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/misc/Progress.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/misc/UnlimitedProgress.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/misc/Utils.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/misc/__init__.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/mySql/MySqlTable.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/mySql/__init__.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/ncList/FileSorter.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/ncList/NCIndex.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/ncList/NCList.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/ncList/NCListCursor.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/ncList/NCListFilePickle.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/ncList/__init__.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/Bins.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/Interval.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/Mapping.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/Sequence.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/SequenceList.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/SubMapping.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/Transcript.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/TranscriptList.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/Python/structure/__init__.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/Java/__init__.pyc
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/__init__.pyc
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Binary file SMART/__init__.pyc has changed
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/Clusterize.xml
--- a/SMART/galaxy/Clusterize.xml Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/galaxy/Clusterize.xml Wed Feb 05 11:51:11 2014 -0500
b
@@ -15,6 +15,8 @@
  -f gff3
  #elif $formatType.FormatInputFileName == 'sam':
  -f sam
+ #elif $formatType.FormatInputFileName == 'bam':
+ -f bam
  #elif $formatType.FormatInputFileName == 'gtf':
  -f gtf
  #end if
@@ -32,6 +34,7 @@
  <option value="gff2">gff2</option>
  <option value="gff3">gff3</option>
  <option value="sam">sam</option>
+ <option value="bam">bam</option>
  <option value="gtf">gtf</option>
  </param>
  <when value="bed">
@@ -49,6 +52,9 @@
  <when value="sam">
  <param name="inputFileName" format="sam" type="data" label="Input File"/>
  </when>
+ <when value="bam">
+ <param name="inputFileName" format="bam" type="data" label="Input File"/>
+ </when>
  <when value="gtf">
  <param name="inputFileName" format="gtf" type="data" label="Input File"/>
  </when>
b
diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/CollapseReads.xml
--- a/SMART/galaxy/CollapseReads.xml Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/galaxy/CollapseReads.xml Wed Feb 05 11:51:11 2014 -0500
b
@@ -15,6 +15,8 @@
  -f gff3
  #elif $formatType.FormatInputFileName == 'sam':
  -f sam
+ #elif $formatType.FormatInputFileName == 'bam':
+ -f bam
  #elif $formatType.FormatInputFileName == 'gtf':
  -f gtf
  #end if
@@ -30,6 +32,7 @@
  <option value="gff2">gff2</option>
  <option value="gff3">gff3</option>
  <option value="sam">sam</option>
+ <option value="bam">bam</option>
  <option value="gtf">gtf</option>
  </param>
  <when value="bed">
@@ -47,6 +50,9 @@
  <when value="sam">
  <param name="inputFileName" format="sam" type="data" label="Input File"/>
  </when>
+ <when value="bam">
+ <param name="inputFileName" format="bam" type="data" label="Input File"/>
+ </when>
  <when value="gtf">
  <param name="inputFileName" format="gtf" type="data" label="Input File"/>
  </when>
b
diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/CompareOverlappingSmallQuery.xml
--- a/SMART/galaxy/CompareOverlappingSmallQuery.xml Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/galaxy/CompareOverlappingSmallQuery.xml Wed Feb 05 11:51:11 2014 -0500
b
@@ -15,6 +15,8 @@
  -f gff3
  #elif $formatType.FormatInputFileName1 == 'sam':
  -f sam
+ #elif $formatType.FormatInputFileName1 == 'bam':
+ -f bam
  #elif $formatType.FormatInputFileName1 == 'gtf':
  -f gtf
  #end if
@@ -29,6 +31,8 @@
  -g gff3
  #elif $formatType2.FormatInputFileName2 == 'sam':
  -g sam
+ #elif $formatType2.FormatInputFileName2 == 'bam':
+ -g bam
  #elif $formatType2.FormatInputFileName2 == 'gtf':
      -g gtf
  #end if
@@ -64,6 +68,7 @@
  <option value="gff2">gff2</option>
  <option value="gff3">gff3</option>
  <option value="sam">sam</option>
+ <option value="bam">bam</option>
  <option value="gtf">gtf</option>
  </param>
  <when value="bed">
@@ -81,6 +86,9 @@
  <when value="sam">
  <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
  </when>
+ <when value="bam">
+ <param name="inputFileName1" format="bam" type="data" label="Input File 1"/>
+ </when>
  <when value="gtf">
  <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
                          </when>
@@ -93,6 +101,7 @@
  <option value="gff2">gff2</option>
  <option value="gff3">gff3</option>
  <option value="sam">sam</option>
+ <option value="bam">bam</option>
  <option value="gtf">gtf</option>
  </param>
  <when value="bed">
@@ -110,6 +119,9 @@
  <when value="sam">
  <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
  </when>
+ <when value="bam">
+ <param name="inputFileName2" format="bam" type="data" label="Input File 2"/>
+ </when>
  <when value="gtf">
  <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
  </when>
b
diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/CompareOverlappingSmallRef.xml
--- a/SMART/galaxy/CompareOverlappingSmallRef.xml Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/galaxy/CompareOverlappingSmallRef.xml Wed Feb 05 11:51:11 2014 -0500
b
@@ -15,6 +15,8 @@
  -f gff3
  #elif $formatType.FormatInputFileName1 == 'sam':
  -f sam
+ #elif $formatType.FormatInputFileName1 == 'bam':
+ -f bam
  #elif $formatType.FormatInputFileName1 == 'gtf':
  -f gtf
  #end if
@@ -29,6 +31,8 @@
  -g gff3
  #elif $formatType2.FormatInputFileName2 == 'sam':
  -g sam
+ #elif $formatType2.FormatInputFileName2 == 'bam':
+ -g bam
  #elif $formatType2.FormatInputFileName2 == 'gtf':
      -g gtf
  #end if
@@ -64,6 +68,7 @@
  <option value="gff2">gff2</option>
  <option value="gff3">gff3</option>
  <option value="sam">sam</option>
+ <option value="bam">bam</option>
  <option value="gtf">gtf</option>
  </param>
  <when value="bed">
@@ -81,6 +86,9 @@
  <when value="sam">
  <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
  </when>
+ <when value="bam">
+ <param name="inputFileName1" format="bam" type="data" label="Input File 1"/>
+ </when>
  <when value="gtf">
  <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
                          </when>
@@ -93,6 +101,7 @@
  <option value="gff2">gff2</option>
  <option value="gff3">gff3</option>
  <option value="sam">sam</option>
+ <option value="bam">bam</option>
  <option value="gtf">gtf</option>
  </param>
  <when value="bed">
@@ -110,6 +119,9 @@
  <when value="sam">
  <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
  </when>
+ <when value="bam">
+ <param name="inputFileName2" format="bam" type="data" label="Input File 2"/>
+ </when>
  <when value="gtf">
  <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
  </when>
b
diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/ConvertTranscriptFile.xml
--- a/SMART/galaxy/ConvertTranscriptFile.xml Fri Jan 10 08:59:23 2014 -0500
+++ b/SMART/galaxy/ConvertTranscriptFile.xml Wed Feb 05 11:51:11 2014 -0500
b
@@ -3,33 +3,14 @@
  <requirements>
  <requirement type="set_environment">PYTHONPATH</requirement>
  </requirements>
-  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName 
-   #if $inputFormatType.FormatInputFileName == 'gff3':
-    -f gff3
-   #elif $inputFormatType.FormatInputFileName == 'bed': 
-   -f bed 
-   #elif $inputFormatType.FormatInputFileName == 'bam': 
-   -f blast
-   #elif $inputFormatType.FormatInputFileName == 'sam': 
-   -f sam
-   #elif $inputFormatType.FormatInputFileName == 'gtf': 
-   -f gtf
-          #end if
-   
-  -g $outputFormatType.outFormat
-   
-   -n $name
-   $strand
-   -o $outputFile
-  
-  </command>
+  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName -f $inputFormatType.FormatInputFileName -g $outputFormatType.outFormat -n $name $strand -o $outputFile </command>
   <inputs>
    <conditional name="inputFormatType">
    <param name="FormatInputFileName"  type="select" label="Input File Format">
    <option value="gff3">GFF3</option> 
    <option value="bed">BED</option> 
+   <option value="sam">SAM</option> 
    <option value="bam">BAM</option> 
-   <option value="sam">SAM</option> 
    <option value="gtf">GTF</option> 
    </param>
    <when value="gff3">  
@@ -38,12 +19,12 @@
    <when value="bed">  
    <param name="inputFileName" format="bed" type="data" label="Input File"/>
    </when>
+   <when value="sam">  
+   <param name="inputFileName" format="sam" type="data" label="Input File"/>
+   </when>
    <when value="bam">  
    <param name="inputFileName" format="bam" type="data" label="Input File"/>
    </when>
-   <when value="sam">  
-   <param name="inputFileName" format="sam" type="data" label="Input File"/>
-   </when>
    <when value="gtf">  
    <param name="inputFileName" format="gtf" type="data" label="Input File"/>
    </when>
b
diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/removeExonLines.xml
--- a/SMART/galaxy/removeExonLines.xml Fri Jan 10 08:59:23 2014 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,18 +0,0 @@
-<tool id="removeExonLines" name="remove exon lines">
-  <description>Removes the lines containing Exon.</description>
- <requirements>
- <requirement type="set_environment">PYTHONPATH</requirement>
- </requirements>
-  <command interpreter="sh"> ../Java/Python/removeExonLines.sh $inputFile > $outputFile  </command>
-  <inputs>
-    <param name="inputFile" type="data" label="Input File" format="gff3"/>
-  </inputs>
-
-  <outputs>
-    <data format="gff3" name="outputFile" label="[remove exon line] output file"/>
-  </outputs>
-
-  <help>
- command example: sh removeExonLines.sh input.gff3
-  </help>
-</tool>
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diff -r 2ac71607aa60 -r 97aa2e42bfdf SMART/galaxy/removeIntrons.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/removeIntrons.xml Wed Feb 05 11:51:11 2014 -0500
[
@@ -0,0 +1,45 @@
+<tool id="removeIntrons" name="remove introns">
+  <description>Removes the introns of the transcript files.</description>
+ <requirements>
+ <requirement type="set_environment">PYTHONPATH</requirement>
+ </requirements>
+  <command interpreter="python"> ../Java/Python/RemoveExons.py -i $formatType.inputFileName -f $formatType.FormatInputFileName -o $outputFile  </command>
+  <inputs>
+ <conditional name="formatType">
+ <param name="FormatInputFileName1" type="select" label="query File Format">
+ <option value="bed">bed</option>
+ <option value="gff">gff</option>
+ <option value="gff2">gff2</option>
+ <option value="gff3">gff3</option>
+ <option value="sam">sam</option>
+ <option value="gtf">gtf</option>
+ </param>
+ <when value="bed">
+ <param name="inputFileName" format="bed" type="data" label="Input File 1"/>
+ </when>
+ <when value="gff">
+ <param name="inputFileName" format="gff" type="data" label="Input File 1"/>
+ </when>
+ <when value="gff2">
+ <param name="inputFileName" format="gff2" type="data" label="Input File 1"/>
+ </when>
+ <when value="gff3">
+ <param name="inputFileName" format="gff3" type="data" label="Input File 1"/>
+ </when>
+ <when value="sam">
+ <param name="inputFileName" format="sam" type="data" label="Input File 1"/>
+ </when>
+ <when value="gtf">
+ <param name="inputFileName" format="gtf" type="data" label="Input File 1"/>
+ </when>
+ </conditional>
+  </inputs>
+
+  <outputs>
+    <data format="gff3" name="outputFile" label="[remove introns] output file"/>
+  </outputs>
+
+  <help>
+ Simply remove the introns of the input file, thus getting the unmatured transcript.
+  </help>
+</tool>
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