# HG changeset patch
# User bgruening
# Date 1376331953 14400
# Node ID 07a5042bbe9032e508b8e3d8255a364643cf1e5b
# Parent e9cd105a8856be3aa5d38339bbb54ce9cef8472f
Uploaded
diff -r e9cd105a8856 -r 07a5042bbe90 homer.py
--- a/homer.py Mon Aug 12 09:06:47 2013 -0400
+++ b/homer.py Mon Aug 12 14:25:53 2013 -0400
@@ -1,14 +1,14 @@
"""
HOMER special datatypes
"""
-
+import os
from galaxy.datatypes.data import get_file_peek
from galaxy.datatypes.data import Text, Data
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.images import Html
-class TagDirectory( Text ):
+class TagDirectory( Html ):
"""Base class for HOMER's Tag Directory datatype."""
file_ext = 'homer_tagdir'
@@ -16,7 +16,7 @@
allow_datatype_change = False
def __init__(self, **kwd):
- Text.__init__( self, **kwd )
+ Html.__init__( self, **kwd )
#self.add_composite_file('tagInfo.txt', description = 'basic configuration information', mimetype = 'text/html') # Contains basic configuration information
self.add_composite_file('tagLengthDistribution.txt', description = 'histogram of read lengths used for alignment', mimetype = 'text/html') # File contains a histogram of read lengths used for alignment.
self.add_composite_file('tagCountDistribution.txt', description = 'histogram of clonal read depth, showing the number of reads per unique position', mimetype = 'text/html') # File contains a histogram of clonal read depth, showing the number of reads per unique position.
@@ -29,25 +29,23 @@
def regenerate_primary_file(self,dataset):
"""
- cannot do this until we are setting metadata
+ regenerate the index file after metadata generation
"""
- flist = os.listdir(dataset.extra_files_path)
- rval = ['CuffDiff Output']
+ rval = ['HOMER database files']
rval.append('')
rval.append('CuffDiff Outputs:')
- for i,fname in enumerate(flist):
+ for fname in os.listdir(dataset.extra_files_path):
sfname = os.path.split(fname)[-1]
rval.append( '- %s' % ( sfname, sfname ) )
rval.append( '
' )
- f = file(dataset.file_name,'w')
- f.write("\n".join( rval ))
- f.write('\n')
+ f = file( dataset.file_name, 'w' )
+ f.write( '%s\n' % '\n'.join( rval ) )
f.close()
-
- def set_meta( self, dataset, **kwd ):
- Text.set_meta( self, dataset, **kwd )
- self.regenerate_primary_file(dataset)
-
+ if not dataset.info:
+ dataset.info = 'HOMER datatype object'
+ if not dataset.blurb:
+ dataset.blurb = 'Composite file - HOMER'
+ return True
def generate_primary_file( self, dataset = None ):
rval = ['HOMER database files']
@@ -59,6 +57,11 @@
rval.append( '
' )
return "\n".join( rval )
+ def set_meta( self, dataset, **kwd ):
+ Html.set_meta( self, dataset, **kwd )
+ self.regenerate_primary_file(dataset)
+
+
def display_data(self, trans, data, preview=False, filename=None,
to_ext=None, size=None, offset=None, **kwd):
"""Apparently an old display method, but still gets called.
diff -r e9cd105a8856 -r 07a5042bbe90 tool-data/homer_available_genomes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/homer_available_genomes.loc.sample Mon Aug 12 14:25:53 2013 -0400
@@ -0,0 +1,6 @@
+hg18
+hg19
+mm9
+mm10
+
+
diff -r e9cd105a8856 -r 07a5042bbe90 tools/findMotifsGenome.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/findMotifsGenome.xml Mon Aug 12 14:25:53 2013 -0400
@@ -0,0 +1,61 @@
+
+
+ blat
+ weblogo
+ ghostscript
+
+
+
+
+ #import tempfile
+ #set $tmpdir = tempfile.mkdtemp()
+ export PATH=\$PATH:$database.fields.path;
+
+ findMotifsGenome $infile ${infile.metadata.dbkey} $tmpdir
+
+
+ ;
+ cp $tmpdir/homerResults.html $denovo_results_html;
+ cp -r $tmpdir/homerResults/* "$denovo_results_html.files_path";
+
+ cp $tmpdir/knownResults.html $known_results_html;
+ cp -r $tmpdir/knownResults/* "$known_results_html.files_path";
+
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+
+ 2>&1
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+ .. class:: infomark
+
+ **Homer findMotifsGenome**
+
+
+
+
diff -r e9cd105a8856 -r 07a5042bbe90 tools/findPeaks.xml
--- a/tools/findPeaks.xml Mon Aug 12 09:06:47 2013 -0400
+++ b/tools/findPeaks.xml Mon Aug 12 14:25:53 2013 -0400
@@ -1,38 +1,40 @@
- homer
+ blat
+ weblogo
+ ghostscript
Homer's peakcaller. Requires tag directories (see makeTagDirectory)
- findPeaks $tagDir.extra_files_path $options -o $outputPeakFile
+ export PATH=\$PATH:$database.fields.path;
- #if $control_tagDir:
- -i $control_tagDir.extra_files_path
+ findPeaks $affected_tag_dir.extra_files_path -o $outputPeakFile
+
+ #if $control_tag_dir:
+ -i $control_tag_dir.extra_files_path
#end if
- 2> $out_log || echo "Error running findPeaks." >&2
+ 2>&1
+
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