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changeset 3:4ea55669f00e draft

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author kevyin
date Tue, 27 Nov 2012 02:33:55 -0500
parents 7268cbc535e5
children 74c1fc7bb164
files README annotatePeaks.xml bed2pos.xml datatypes_conf.xml findPeaks.xml homerDatatypes.py makeTagDirectory.xml pos2bed.xml
diffstat 8 files changed, 0 insertions(+), 349 deletions(-) [+]
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--- a/README	Fri Nov 23 00:30:27 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-Homer wrapper for Galaxy
-
-Code repo: https://bitbucket.org/gvl/homer
-
-=========================================:
-LICENSE for this wrapper: 
-=========================================:
-Kevin Ying
-Garvan Institute: http://www.garvan.org.au
-GVL: https://genome.edu.au/wiki/GVL
-
-http://opensource.org/licenses/mit-license.php
-
--- a/annotatePeaks.xml	Fri Nov 23 00:30:27 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-<tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.2">
-    <requirements>
-        <requirement type="package">homer</requirement>
-    </requirements>
-    <description></description>
-    <!--<version_command></version_command>-->
-    <command>
-        annotatePeaks.pl $input_bed $genome_selector 1&gt; $out_annotated
-        2&gt; $out_log || echo "Error running annotatePeaks." >&amp;2
-    </command>
-    <inputs>
-        <param format="tabular,bed" name="input_bed" type="data" label="Homer peak positions or BED format" />
-        <param name="genome_selector" type="select" label="Genome version">
-            <option value="hg19" selected="true">hg19</option>
-        </param>
-    </inputs>
-    <outputs>
-        <!--<data format="html" name="html_outfile" label="index" />-->
-        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
-        <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" />
-        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.log" />
-    </outputs>
-    <tests>
-        <test>
-            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
-            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
-        </test>
-    </tests>
-
-    <help>
-
-        .. class:: infomark
-
-        **Homer annoatePeaks**
-        More information on accepted formats
-        http://biowhat.ucsd.edu/homer/ngs/annotation.html
-
-
-    </help>
-</tool>
-
--- a/bed2pos.xml	Fri Nov 23 00:30:27 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-<tool id="homer_bed2pos" name="homer_bed2pos" version="0.0.2">
-    <requirements>
-        <requirement type="package">homer</requirement>
-    </requirements>
-    <description></description>
-    <!--<version_command></version_command>-->
-    <command>
-        bed2pos.pl $input_bed 1&gt; $out_pos
-        2&gt; $out_log || echo "Error running bed2pos." >&amp;2
-    </command>
-    <inputs>
-        <param format="tabular,bed" name="input_bed" type="data" label="BED file" />
-    </inputs>
-    <outputs>
-        <!--<data format="html" name="html_outfile" label="index" />-->
-        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
-        <data format="tabular" name="out_pos" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#" />
-        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#.log" />
-    </outputs>
-    <tests>
-        <test>
-            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
-            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
-        </test>
-    </tests>
-
-    <help>
-        .. class:: infomark
-
-        **Homer bed2pos.pl**
-        http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
-    </help>
-</tool>
-
--- a/datatypes_conf.xml	Fri Nov 23 00:30:27 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-  <datatype_files>
-    <datatype_file name="homerDatatypes.py"/>
-  </datatype_files>
-  <registration>
-    <datatype extension="homerTagDirectory" type="galaxy.datatypes.homerDatatypes:HomerTagDirectory" display_in_upload="False" mimetype="text/html"/>
-  </registration>
-</datatypes>
--- a/findPeaks.xml	Fri Nov 23 00:30:27 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-<tool id="homer_findPeaks" name="homer_findPeaks" version="0.0.7">
-    <requirements>
-        <requirement type="package">homer</requirement>
-    </requirements>
-    <description></description>
-    <!--<version_command></version_command>-->
-    <command>
-        findPeaks $tagDir.extra_files_path $options -o $outputPeakFile
-
-    #if $control_tagDir:
-        -i $control_tagDir.extra_files_path
-    #end if
-
-        2&gt; $out_log || echo "Error running findPeaks." >&amp;2
-    </command>
-    <inputs>
-        <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" />
-        <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" />
-        <param type="text" name="options" label="Extra options" value="" >
-          <sanitizer>
-            <valid initial="string.printable">
-             <remove value="&apos;"/>
-            </valid>
-            <mapping initial="none">
-              <add source="&apos;" target="__sq__"/>
-            </mapping>
-          </sanitizer>
-        </param>
-    </inputs>
-    <outputs>
-        <!--<data format="html" name="html_outfile" label="index" />-->
-        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
-        <data format="txt" name="outputPeakFile" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.txt" />
-        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.log" />
-    </outputs>
-    <tests>
-        <test>
-            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
-            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
-        </test>
-    </tests>
-
-    <help>
-
-  .. class:: infomark
-
-  **Homer findPeaks**
-  http://biowhat.ucsd.edu/homer/ngs/peaks.html
-
-    </help>
-</tool>
-
--- a/homerDatatypes.py	Fri Nov 23 00:30:27 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,118 +0,0 @@
-"""
-homer composite datatypes 
-Use at your peril
-Kevin Ying
-for the homer wrapper
-
-Nov 2012
-"""
-
-import logging, os, sys, time, tempfile, shutil, string, glob
-import data
-from galaxy import util
-from cgi import escape
-import urllib, binascii
-from galaxy.web import url_for
-from galaxy.datatypes import metadata
-from galaxy.datatypes.metadata import MetadataElement
-from galaxy.datatypes.data import Text
-from galaxy.datatypes.tabular import Tabular
-from galaxy.datatypes.images import Html
-from galaxy.datatypes.interval import Interval
-from galaxy.util.hash_util import *
-
-gal_Log = logging.getLogger(__name__)
-verbose = False
-
-class HomerTagDirectory(Html):
-    """
-    base class to use for homer tag directory datatypes
-    composite datatype elements
-    stored in extra files path
-    """
-   
-    #MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default='HomerTagDirectory',
-    #readonly=True, set_in_upload=False)
-    
-    composite_type = 'auto_primary_file'
-    #allow_datatype_change = False
-    file_ext = 'homerTagDirectory'
-
-    def __init__(self, **kwd):
-        Html.__init__(self, **kwd)
-        self.add_composite_file('tagInfo.txt', description="tagInfo")
-        self.add_composite_file('tagAutocorrelation.txt', description="tagAutocorrelation")
-        self.add_composite_file('tagCountDistribution.txt', description="tagCountDistribution")
-        self.add_composite_file('tagLengthDistribution.txt', description="tagLengthDistribution")
-
-    def generate_primary_file(self, dataset=None):
-        rval = ['<html><head><title>Homer Tag Directory Galaxy Composite Dataset </title></head><p/>']
-        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
-        for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
-            fn = composite_name
-            opt_text = ''
-            if composite_file.optional:
-                opt_text = ' (optional)'
-            if composite_file.get('description'):
-                rval.append( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
-            else:
-                rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) )
-        rval.append( '</ul></div></html>' )
-        return "\n".join( rval )
-
-
-    def regenerate_primary_file(self,dataset):
-        """
-        cannot do this until we are setting metadata 
-        """
-        #bn = dataset.metadata.base_name
-        efp = dataset.extra_files_path
-        flist = os.listdir(efp)
-        rval = ['<html><head><title>Files for Composite Dataset %s</title></head><body><p/>Composite %s contains:<p/><ul>' % (dataset.name,dataset.name)]
-        for i,fname in enumerate(flist):
-            sfname = os.path.split(fname)[-1] 
-            f,e = os.path.splitext(fname)
-            rval.append( '<li><a href="%s">%s</a></li>' % ( sfname, sfname) )
-        rval.append( '</ul></body></html>' )
-        f = file(dataset.file_name,'w')
-        f.write("\n".join( rval ))
-        f.write('\n')
-        f.close()
-
-    def get_mime(self):
-        """Returns the mime type of the datatype"""
-        return 'text/html'
-
-    def set_meta( self, dataset, **kwd ):
-
-        """
-        for homer maketagdirectory eg
-
-        """
-        Html.set_meta( self, dataset, **kwd )
-        if kwd.get('overwrite') == False:
-            if verbose:
-                gal_Log.debug('@@@ HomerTagDirectory set_meta called with overwrite = False')
-            return True
-        try:
-            efp = dataset.extra_files_path
-        except: 
-            if verbose:                
-               gal_Log.debug('@@@ HomerTagDirectory set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
-            return False
-        try:
-            flist = os.listdir(efp)
-        except:
-            if verbose: gal_Log.debug('@@@ HomerTagDirectory set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name))
-            return False
-        if len(flist) == 0:
-            if verbose:
-                gal_Log.debug('@@@ HomerTagDirectory set_meta failed - %s efp %s is empty?' % (dataset.name,efp))
-            return False
-        self.regenerate_primary_file(dataset)
-        if not dataset.info:           
-                dataset.info = 'Galaxy HomerTagDirectory datatype object'
-        if not dataset.blurb:
-               dataset.blurb = 'Composite file - Homer Galaxy toolkit'
-        return True
-
--- a/makeTagDirectory.xml	Fri Nov 23 00:30:27 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="0.0.8">
-    <requirements>
-        <requirement type="package" >homer</requirement>
-    </requirements>
-    <description>makeTagDirectory</description>
-    <version_command>echo "Doh!"</version_command>
-    <command> makeTagDirectory ${tagDir.extra_files_path}
-        #for $alignF in $alignmentFiles
-          $alignF.file -format $alignF.file.ext
-        #end for
-        2&gt; $out_log || echo "Error running homer_makeTagDirectory." >&amp;2
-
-    </command>
-    <inputs>
-        <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />
-        <repeat name="alignmentFiles" title="Alignment Files">
-          <param name="file" label="Add file" type="data" format="sam,bed" />
-        </repeat>
-    </inputs>
-    <outputs>
-        <data format="homerTagDirectory" name="tagDir" label="${title}" />
-        <data format="txt" name="out_log" label="${title}.log" />
-        <!--<data format="html" name="html_outfile" label="index" />-->
-        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
-    </outputs>
-
-
-    <tests>
-        <!--<test>-->
-            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
-            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
-        <!--</test>-->
-    </tests>
-
-    <help>
-
-        .. class:: infomark
-
-        After the job finishes, save the zip file, unzip and open "index.html"
-
-        The actual meme-chip command is displayed under "Command line summary"
-
-        Defaults:
-        http://meme.nbcr.net/meme/doc/meme-chip.html
-
-    </help>
-</tool>
-
--- a/pos2bed.xml	Fri Nov 23 00:30:27 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-<tool id="homer_pos2bed" name="homer_pos2bed" version="0.0.2">
-    <requirements>
-        <requirement type="package">homer</requirement>
-    </requirements>
-    <description></description>
-    <!--<version_command></version_command>-->
-    <command>
-        pos2bed.pl $input_peak 1&gt; $out_bed
-        2&gt; $out_log || echo "Error running pos2bed." >&amp;2
-    </command>
-    <inputs>
-        <param format="tabular" name="input_peak" type="data" label="Homer peak positions" />
-    </inputs>
-    <outputs>
-        <!--<data format="html" name="html_outfile" label="index" />-->
-        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
-        <data format="bed" name="out_bed" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.bed" />
-        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.log" />
-    </outputs>
-    <tests>
-        <test>
-            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
-            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
-        </test>
-    </tests>
-
-    <help>
-        .. class:: infomark
-
-        **Homer pos2bed.pl**
-        http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
-    </help>
-</tool>
-