Adding back 'wiggle to interval' converter

datatypes_conf.xml.sample

@@ -58,6 +58,7 @@
         <datatype extension="txtseq.zip" type="galaxy.datatypes.data:Txtseq" mimetype="application/zip" display_in_upload="true"/>
         <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true">
             <converter file="wiggle_to_array_tree_converter.xml" target_datatype="array_tree"/>
+            <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/>
         </datatype>
         <datatype extension="array_tree" type="galaxy.datatypes.data:Data" />
         <datatype extension="interval_index" type="galaxy.datatypes.data:Data" />

lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+#code is same as ~/tools/stats/wiggle_to_simple.py
+
+"""
+Read a wiggle track and print out a series of lines containing
+"chrom position score". Ignores track lines, handles bed, variableStep
+and fixedStep wiggle lines.
+"""
+import sys
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+import bx.wiggle
+from galaxy.tools.exception_handling import *
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def main():
+    if len( sys.argv ) > 1: 
+        in_file = open( sys.argv[1] )
+    else: 
+        in_file = open( sys.stdin )
+    
+    if len( sys.argv ) > 2:
+        out_file = open( sys.argv[2], "w" )
+    else:
+        out_file = sys.stdout
+    
+    try:
+        for fields in bx.wiggle.IntervalReader( UCSCOutWrapper( in_file ) ):
+            out_file.write( "%s\n" % "\t".join( map( str, fields ) ) )
+    except UCSCLimitException:
+        # Wiggle data was truncated, at the very least need to warn the user.
+        print 'Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.'
+    except ValueError, e:
+        in_file.close()
+        out_file.close()
+        stop_err( str( e ) )
+
+    in_file.close()
+    out_file.close()
+
+if __name__ == "__main__": main()

lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml

@@ -0,0 +1,11 @@
+<tool id="CONVERTER_wiggle_to_interval_0" name="Wiggle to Interval">
+  <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
+  <!-- Used on the metadata edit page. -->
+  <command interpreter="python">wiggle_to_simple_converter.py $input $out_file1 </command>
+  <inputs>
+    <param format="wig" name="input" type="data" label="Convert"/>
+  </inputs>
+  <outputs>
+    <data format="interval" name="out_file1" />
+  </outputs>
+</tool>

tool_conf.xml.main

@@ -47,6 +47,7 @@
     <tool file="maf/maf_to_fasta.xml" />
     <tool file="fasta_tools/tabular_to_fasta.xml" />
     <tool file="fastx_toolkit/fastq_to_fasta.xml" />
+    <tool file="filters/wiggle_to_simple.xml" />
   </section>
   <section name="FASTA manipulation" id="fasta_manipulation">
     <tool file="fasta_tools/fasta_compute_length.xml" />

tool_conf.xml.sample

@@ -71,6 +71,7 @@
     <tool file="maf/maf_to_fasta.xml" />
     <tool file="fasta_tools/tabular_to_fasta.xml" />
     <tool file="fastx_toolkit/fastq_to_fasta.xml" />
+    <tool file="filters/wiggle_to_simple.xml" />
   </section>
   <section name="Extract Features" id="features">
     <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />

tools/filters/wiggle_to_simple.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+
+"""
+Read a wiggle track and print out a series of lines containing
+"chrom position score". Ignores track lines, handles bed, variableStep
+and fixedStep wiggle lines.
+"""
+import sys
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+import bx.wiggle
+from galaxy.tools.exception_handling import *
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def main():
+    if len( sys.argv ) > 1: 
+        in_file = open( sys.argv[1] )
+    else: 
+        in_file = open( sys.stdin )
+    
+    if len( sys.argv ) > 2:
+        out_file = open( sys.argv[2], "w" )
+    else:
+        out_file = sys.stdout
+    
+    try:
+        for fields in bx.wiggle.IntervalReader( UCSCOutWrapper( in_file ) ):
+            out_file.write( "%s\n" % "\t".join( map( str, fields ) ) )
+    except UCSCLimitException:
+        # Wiggle data was truncated, at the very least need to warn the user.
+        print 'Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.'
+    except ValueError, e:
+        in_file.close()
+        out_file.close()
+        stop_err( str( e ) )
+
+    in_file.close()
+    out_file.close()
+
+if __name__ == "__main__": main()

tools/filters/wiggle_to_simple.xml

@@ -0,0 +1,88 @@
+<tool id="wiggle2simple1" name="Wiggle-to-Interval">
+  <description>converter</description>
+  <command interpreter="python">wiggle_to_simple.py $input $out_file1 </command>
+  <inputs>
+    <param format="wig" name="input" type="data" label="Convert"/>
+  </inputs>
+  <outputs>
+    <data format="interval" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="2.wig" />
+      <output name="out_file1" file="2.interval"/>
+    </test>
+    <test>
+      <param name="input" value="3.wig" />
+      <output name="out_file1" file="3_wig.bed"/>
+    </test>
+  </tests>
+  <help>
+**Syntax**
+
+This tool converts wiggle data into interval type.
+
+- **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line.  Following the track definition line is the track data, which can be entered in three different formats described below.
+
+  - **BED format** with no declaration line and four columns of data::
+
+      chromA  chromStartA  chromEndA  dataValueA
+      chromB  chromStartB  chromEndB  dataValueB
+
+  - **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values::
+
+      variableStep  chrom=chrN  [span=windowSize]
+      chromStartA  dataValueA
+      chromStartB  dataValueB
+
+  - **fixedStep** single column data; started by a declaration line and followed with data values::
+
+      fixedStep  chrom=chrN  start=position  step=stepInterval  [span=windowSize]
+      dataValue1
+      dataValue2
+
+-----
+
+**Example**
+
+- input wiggle format file::
+
+    #track type=wiggle_0 name="Bed Format" description="BED format"
+    chr19 59302000 59302300 -1.0
+    chr19 59302300 59302600 -0.75
+    chr19 59302600 59302900 -0.50
+    chr19 59302900 59303200 -0.25
+    chr19 59303200 59303500 0.0
+    #track type=wiggle_0 name="variableStep" description="variableStep format"
+    variableStep chrom=chr19 span=150
+    59304701 10.0
+    59304901 12.5
+    59305401 15.0
+    59305601 17.5
+    #track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full
+    fixedStep chrom=chr19 start=59307401 step=300 span=200
+    1000
+    900
+    800
+    700
+    600
+
+- convert the above file to interval file::
+
+    chr19	59302000	59302300	+	-1.0
+    chr19	59302300	59302600	+	-0.75
+    chr19	59302600	59302900	+	-0.5
+    chr19	59302900	59303200	+	-0.25
+    chr19	59303200	59303500	+	0.0
+    chr19	59304701	59304851	+	10.0
+    chr19	59304901	59305051	+	12.5
+    chr19	59305401	59305551	+	15.0
+    chr19	59305601	59305751	+	17.5
+    chr19	59307701	59307901	+	1000.0
+    chr19	59308001	59308201	+	900.0
+    chr19	59308301	59308501	+	800.0
+    chr19	59308601	59308801	+	700.0
+    chr19	59308901	59309101	+	600.0
+
+</help>
+</tool>