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changeset 13:d0220fea2b51 draft

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author kevyin
date Mon, 17 Dec 2012 00:46:22 -0500
parents 4356089c8e7f
children d9658163c29e
files README annotatePeaks.xml bed2pos.xml findPeaks.xml makeTagDirectory.py makeTagDirectory.xml pos2bed.xml tool_dependencies.xml
diffstat 8 files changed, 0 insertions(+), 374 deletions(-) [+]
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--- a/README	Mon Dec 17 00:25:28 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	Mon Dec 17 00:25:28 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-<tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.4">
-    <requirements>
-        <requirement type="package" version="4.1">homer</requirement>
-    </requirements>
-    <description></description>
-    <!--<version_command></version_command>-->
-    <command>
-        annotatePeaks.pl $input_bed $genome_selector 1&gt; $out_annotated
-        2&gt; $out_log || echo "Error running annotatePeaks." >&amp;2
-    </command>
-    <inputs>
-        <param format="tabular,bed" name="input_bed" type="data" label="Homer peaks OR BED format"/>
-        <param name="genome_selector" type="select" label="Genome version">
-            <option value="hg19" selected="true">hg19</option>
-        </param>
-        <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options">
-          <sanitizer>
-            <valid initial="string.printable">
-             <remove value="&apos;"/>
-             <remove value="/"/>
-            </valid>
-            <mapping initial="none">
-              <add source="&apos;" target="__sq__"/>
-            </mapping>
-          </sanitizer>
-        </param>
-    </inputs>
-    <outputs>
-        <!--<data format="html" name="html_outfile" label="index" />-->
-        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
-        <data format="csv" name="out_annotated" label="${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 and options
-
-        http://biowhat.ucsd.edu/homer/ngs/annotation.html
-
-        TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format.
-
-    </help>
-</tool>
-
--- a/bed2pos.xml	Mon Dec 17 00:25:28 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-<tool id="homer_bed2pos" name="homer_bed2pos" version="0.0.3">
-    <requirements>
-        <requirement type="package" version="4.1">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
-
-        Converts: BED -(to)-> homer peak positions
-
-        **Homer bed2pos.pl**
-
-        http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
-    </help>
-</tool>
-
--- a/findPeaks.xml	Mon Dec 17 00:25:28 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-<tool id="homer_findPeaks" name="homer_findPeaks" version="0.1.2">
-    <requirements>
-        <requirement type="package" version="4.1">homer</requirement>
-    </requirements>
-    <description>Homer's peakcaller. Requires tag directories (see makeTagDirectory)</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; $out_log || echo "Error running findPeaks." >&amp;2
-    </command>
-    <inputs>
-        <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" help="Must be made with homer_makeTagDirectory" />
-        <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" help="Must be made with homer_makeTagDirectory" />
-        <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options">
-          <sanitizer>
-            <valid initial="string.printable">
-             <remove value="&apos;"/>
-             <remove value="/"/>
-            </valid>
-            <mapping initial="none">
-              <add source="&apos;" target="__sq__"/>
-            </mapping>
-          </sanitizer>
-        </param>
-    </inputs>
-    <outputs>
-        <!--<data format="html" name="html_outfile" label="index" />-->
-        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
-        <data format="txt" name="outputPeakFile" label="${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**
-
-  For more options, look under: "Command line options for findPeaks"
-
-  http://biowhat.ucsd.edu/homer/ngs/peaks.html
-
-  TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format.
-
-    </help>
-</tool>
-
--- a/makeTagDirectory.py	Mon Dec 17 00:25:28 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-"""
-
-
-"""
-import re
-import os
-import sys
-import subprocess
-import optparse
-import shutil
-import tempfile
-
-def getFileString(fpath, outpath):
-    """
-    format a nice file size string
-    """
-    size = ''
-    fp = os.path.join(outpath, fpath)
-    s = '? ?'
-    if os.path.isfile(fp):
-        n = float(os.path.getsize(fp))
-        if n > 2**20:
-            size = ' (%1.1f MB)' % (n/2**20)
-        elif n > 2**10:
-            size = ' (%1.1f KB)' % (n/2**10)
-        elif n > 0:
-            size = ' (%d B)' % (int(n))
-        s = '%s %s' % (fpath, size) 
-    return s
-
-class makeTagDirectory():
-    """wrapper
-    """
-
-    def __init__(self,opts=None, args=None):
-        self.opts = opts
-        self.args = args
-        
-    def run_makeTagDirectory(self):
-        """
-        makeTagDirectory <Output Directory Name> [options] <alignment file1> [alignment file 2] 
-
-        """
-        if self.opts.format != "bam":
-            cl = [self.opts.executable] + args + ["-format" , self.opts.format]
-        else:
-            cl = [self.opts.executable] + args
-        print cl
-        p = subprocess.Popen(cl)
-        retval = p.wait()
-
-
-        html = self.gen_html(args[0])
-        #html = self.gen_html()
-        return html,retval
-
-    def gen_html(self, dr=os.getcwd()):
-        flist = os.listdir(dr)
-        print flist
-        """ add a list of all files in the tagdirectory
-        """
-        res = ['<div class="module"><h2>Files created by makeTagDirectory</h2><table cellspacing="2" cellpadding="2">\n']
-
-        flist.sort()
-        for i,f in enumerate(flist):
-             if not(os.path.isdir(f)):
-                 fn = os.path.split(f)[-1]
-                 res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, dr)))
-
-        res.append('</table>\n') 
-
-        return res
-
-if __name__ == '__main__':
-    op = optparse.OptionParser()
-    op.add_option('-e', '--executable', default='makeTagDirectory')
-    op.add_option('-o', '--htmloutput', default=None)
-    op.add_option('-f', '--format', default="sam")
-    opts, args = op.parse_args()
-    #assert os.path.isfile(opts.executable),'## makeTagDirectory.py error - cannot find executable %s' % opts.executable
-
-    #if not os.path.exists(opts.outputdir): 
-        #os.makedirs(opts.outputdir)
-    f = makeTagDirectory(opts, args)
-
-    html,retval = f.run_makeTagDirectory()
-    f = open(opts.htmloutput, 'w')
-    f.write(''.join(html))
-    f.close()
-    if retval <> 0:
-         print >> sys.stderr, serr # indicate failure
-    
-
-
--- a/makeTagDirectory.xml	Mon Dec 17 00:25:28 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1">
-    <requirements>
-        <requirement type="package" version="4.1">homer</requirement>
-    </requirements>
-    <description>Simple wrapper for makeTagDirectory. Used by findPeaks</description>
-    <!--<version_command></version_command>-->
-    <command interpreter="python">makeTagDirectory.py ${tagDir.files_path} 
-        #for $alignF in $alignmentFiles
-          $alignF.file -f $alignF.file.ext
-        #end for
-          -o $tagDir
-        2&gt; $out_log || echo "Error running homer_makeTagDirectory." >&amp;2
-
-    </command>
-    <inputs>
-        <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />
-        <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options">
-          <sanitizer>
-            <valid initial="string.printable">
-             <remove value="&apos;"/>
-             <remove value="/"/>
-            </valid>
-            <mapping initial="none">
-              <add source="&apos;" target="__sq__"/>
-            </mapping>
-          </sanitizer>
-        </param>
-        <repeat name="alignmentFiles" title="Alignment Files">
-          <param name="file" label="Add file" type="data" format="sam,bed" />
-        </repeat>
-    </inputs>
-    <outputs>
-        <!--<data format="homerTagDirectory" name="tagDir" label="${title} tag directory" />-->
-        <data format="html" name="tagDir" label="${title} tag directory" />
-        <data format="txt" name="out_log" label="${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
-
-  **Homer makeTagDirectory**
-
-  For more options, look under: "Command line options"
-
-  http://biowhat.ucsd.edu/homer/ngs/tagDir.html
-
-
-    </help>
-</tool>
-
--- a/pos2bed.xml	Mon Dec 17 00:25:28 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-<tool id="homer_pos2bed" name="homer_pos2bed" version="0.0.3">
-    <requirements>
-        <requirement type="package" version="4.1" >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($input_peak.name))[0]#.log" />
-    </outputs>
-    <tests>
-        <test>
-            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
-            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
-        </test>
-    </tests>
-
-    <help>
-        .. class:: infomark
-
-        Converts: homer peak positions -(to)-> BED format
-
-        **Homer pos2bed.pl**
-
-        http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
-    </help>
-</tool>
-
--- a/tool_dependencies.xml	Mon Dec 17 00:25:28 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="homer">
-    <install version="4.1">
-      <actions>
-        <action type="download_by_url">http://biowhat.ucsd.edu/homer/configureHomer.pl</action>
-        <action type="shell_command">perl ./configureHomer.pl -install</action>
-        <action type="shell_command">perl ./configureHomer.pl -install hg19</action>
-        <action type="set_environment">
-          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-        </action>
-      </actions>
-    </install>
-    <readme>
-      Installs homer
-    </readme>
-  </package>
-</tool_dependency>
-