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changeset 6:d13d6542ea7e

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Deleted selected files
author cjav
date Tue, 14 Feb 2012 16:37:48 -0500
parents bcd2194a2de1
children fa50a3392110
files cummerbund_wrapper.py cummerbund_wrapper.xml
diffstat 2 files changed, 0 insertions(+), 379 deletions(-) [+]
line wrap: on
line diff
--- a/cummerbund_wrapper.py	Tue Feb 14 16:19:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,77 +0,0 @@
-#!/usr/bin/env python
-
-### Runs "r_script" and generates a HTML report
-### Inspired on cuffdiff_wrapper.py and gatk_wrapper.py
-### Carlos Borroto <carlos.borroto@gmail.com>
-
-import optparse, os, shutil, subprocess, sys, tempfile
-
-def stop_err( msg ):
-    sys.stderr.write( "%s\n" % msg )
-    sys.exit()
-
-def html_report_from_directory( html_out, dir ):
-    html_out.write( '<html>\n<head>\n<title>Galaxy - cummeRbund Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' )
-    for fname in sorted( os.listdir( dir ) ):
-        html_out.write(  '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
-    html_out.write( '</ul>\n</body>\n</html>\n' )
-
-def __main__():
-    #Parse Command Line
-    parser = optparse.OptionParser()
-
-    # wrapper options
-    parser.add_option('', '--r-script', dest='r_script', help='R script')
-    parser.add_option('', '--html-report-from-directory', dest='html_report_from_directory', type="string", nargs=2, help='"Target HTML File" "Directory"')
-        
-    (options, args) = parser.parse_args()
-    
-    (html_filename, html_dir) = options.html_report_from_directory
-    
-    # Make html report directory for output.
-    os.mkdir( html_dir )
-    
-    # Make a tmp dir
-    tmp_dir = tempfile.mkdtemp( prefix='tmp-cummeRbund-' )
-    
-    # Build command.
-    cmd = ( "Rscript --vanilla %s" % options.r_script )
-    
-    # Debugging.
-    print cmd
-    
-    # Run command.
-    try:
-        tmp_name = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
-        tmp_stderr = open( tmp_name, 'wb' )
-        proc = subprocess.Popen( args=cmd, shell=True, cwd=html_dir, stderr=tmp_stderr.fileno() )
-        returncode = proc.wait()
-        tmp_stderr.close()
-        
-        # Get stderr, allowing for case where it's very large.
-        tmp_stderr = open( tmp_name, 'rb' )
-        stderr = ''
-        buffsize = 1048576
-        try:
-            while True:
-                stderr += tmp_stderr.read( buffsize )
-                if not stderr or len( stderr ) % buffsize != 0:
-                    break
-        except OverflowError:
-            pass
-        tmp_stderr.close()
-        
-        # Error checking.
-        if returncode != 0:
-            raise Exception, stderr
-    except Exception, e:
-        stop_err( 'Error running R script. ' + str( e ) )
-    
-    # write the html report
-    html_report_from_directory( open( html_filename, 'wb' ), html_dir )
-    
-    # Clean up temp dirs
-    if os.path.exists( tmp_dir ):
-        shutil.rmtree( tmp_dir )
-
-if __name__=="__main__": __main__()
--- a/cummerbund_wrapper.xml	Tue Feb 14 16:19:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,302 +0,0 @@
-<tool id="cummerbund" name="cummeRbund" version="0.0.3">
-    
-    <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description>
-    
-    <command interpreter="python">
-        cummerbund_wrapper.py
-            --r-script ${script_file}
-            --html-report-from-directory "${output_html}" "${output_html.files_path}"
-    </command>
-    
-    <inputs>
-        <conditional name="backend_database_source">
-            <param name="backend_database_selector" type="select" label="Will you select a backend database file from the history or do you want to build a new one using cuffdiff output?">
-                <option value="history" selected="true">Use backend database from the history</option>
-                <option value="cuffdiff_output">Build backend database using cuffdiff output</option>
-            </param>
-            <when value="cuffdiff_output">
-                <param format="tabular" name="isoforms_fpkm_tracking" type="data" label="Transcript FPKM tracking"/>
-                <param format="tabular" name="isoforms_exp" type="data" label="Transcript differential expression testing"/>
-                <param format="tabular" name="genes_fpkm_tracking" type="data" label="Gene FPKM tracking"/>
-                <param format="tabular" name="genes_exp" type="data" label="Gene differential expression testing"/>
-                <param format="tabular" name="tss_groups_fpkm_tracking" type="data" label="TSS groups FPKM tracking"/>
-                <param format="tabular" name="tss_groups_exp" type="data" label="TSS groups differential expression testing"/>
-                <param format="tabular" name="cds_fpkm_tracking" type="data" label="CDS FPKM tracking"/>
-                <param format="tabular" name="cds_exp_diff" type="data" label="CDS FPKM differential expression testing"/>
-                <param format="tabular" name="cds_diff" type="data" label="CDS overloading diffential expression testing"/>
-                <param format="tabular" name="promoters_diff" type="data" label="Promoters differential expression testing"/>
-                <param format="tabular" name="splicing_diff" type="data" label="Splicing differential expression testing"/>
-                <param name="rebuild" type="hidden" value="TRUE"/>
-            </when>
-            <when value="history">
-                <param name="input_database" type="data" format="data" label="Select backend database (sqlite)"/>
-            </when>
-        </conditional>
-        <repeat name="plots" title="Plots">
-			<param name="width" type="text" value="1280" label="The width of the image"/>
-			<param name="height" type="text" value="960" label="The height of the image"/>
-			<conditional name="plot">
-				<param name="type" type="select" label="Plot type">
-					<option value="density" selected="true">Density</option>
-					<option value="boxplot">Boxplot</option>
-					<option value="scatter">Scatter</option>
-					<option value="volcano">Volcano</option>
-					<option value="heatmap">Heatmap</option>
-					<option value="cluster">Cluster</option>
-					<option value="expressionplot">Expression Plot</option>
-					<option value="expressionbarplot">Expression Bar Plot</option>
-				</param>
-				<when value="density">
-					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
-				</when>
-				<when value="boxplot">
-					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
-				</when>
-				<when value="scatter">
-					<param name="x" type="text" label="Sample name for x axis"/>
-					<param name="y" type="text" label="Sample name for y axis"/>
-					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
-					<param name="smooth" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Add a smooth-fit regression line"/>
-					<conditional name="multiple_genes">
-						<param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/>
-						<when value="T">
-                            <param name="features" type="select" label="Expression levels to plot?">
-                                <option value="gene" selected="true">Genes</option>
-                                <option value="isoforms">Isoforms</option>
-                                <option value="tss">TSS</option>
-                                <option value="cds">CDS</option>
-                            </param>
-							<repeat name="genes" title="Genes">
-								<param name="gene_id" type="text" label="Gene ID"/>
-							</repeat> 
-						</when>
-                        <when value="F"/>
-					</conditional>
-				</when>
-				<when value="volcano">
-					<param name="x" type="text" label="First sample name for comparison"/>
-					<param name="y" type="text" label="Second sample name for comparison"/>
-					<conditional name="multiple_genes">
-						<param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/>
-						<when value="T">
-                            <param name="features" type="select" label="Expression levels to plot?">
-                                <option value="gene" selected="true">Genes</option>
-                                <option value="isoforms">Isoforms</option>
-                                <option value="tss">TSS</option>
-                                <option value="cds">CDS</option>
-                            </param>
-							<repeat name="genes" title="Genes">
-								<param name="gene_id" type="text" label="Gene ID"/>
-							</repeat> 
-						</when>
-                        <when value="F"/>
-					</conditional>
-				</when>
-				<when value="heatmap">
-					<param name="features" type="select" label="Expression levels to plot?">
-						<option value="gene" selected="true">Genes</option>
-						<option value="isoforms">Isoforms</option>
-						<option value="tss">TSS</option>
-						<option value="cds">CDS</option>
-					</param>
-					<repeat name="genes" title="Genes">
-						<param name="gene_id" type="text" label="Gene ID"/>
-					</repeat>
-					<param name="clustering" type="select" label="Cluster by">
-						<option value="row">Row</option>
-						<option value="column">Column</option>
-						<option value="both" selected="true">Both</option>
-						<option value="none">None</option>
-					</param>
-					<param name="labcol" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/>
-					<param name="labrow" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/>
-					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
-					<param name="border" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw border around plot?"/>
-				</when>
-				<when value="cluster">
-					<param name="features" type="select" label="Expression levels to plot?">
-						<option value="gene" selected="true">Genes</option>
-						<option value="isoforms">Isoforms</option>
-						<option value="tss">TSS</option>
-						<option value="cds">CDS</option>
-					</param>
-					<repeat name="genes" title="Genes">
-						<param name="gene_id" type="text" label="Gene ID"/>
-					</repeat>
-                    <param name="k" type="text" label="Number of pre-defined clusters to attempt to find."/>
-                    <param name="iter_max" type="text" value="100" label="Max iterations"/>
-				</when>
-				<when value="expressionplot">
-					<param name="features" type="select" label="Expression levels to plot?">
-						<option value="gene" selected="true">Genes</option>
-						<option value="isoforms">Isoforms</option>
-						<option value="tss">TSS</option>
-						<option value="cds">CDS</option>
-					</param>
-					<param name="gene_id" type="text" label="Gene ID"/>
-					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
-                    <param name="draw_summary" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw a 'summary' line with mean FPKM
-          values for each condition?"/>
-                    <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/>
-				</when>
-				<when value="expressionbarplot">
-					<param name="features" type="select" label="Expression levels to plot?">
-						<option value="gene" selected="true">Genes</option>
-						<option value="isoforms">Isoforms</option>
-						<option value="tss">TSS</option>
-						<option value="cds">CDS</option>
-					</param>
-					<param name="gene_id" type="text" label="Gene ID"/>
-					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
-                    <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/>
-				</when>
-			</conditional>
-		</repeat>
-    </inputs>
-    
-    <outputs>
-        <data format="data" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)">
-            <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter>
-        </data>
-    	<data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/>
-    </outputs>
-
-    <requirements>
-        <requirement type="binary">R</requirement>
-    </requirements>
-
-<!-->
-  <tests>
-    <test>
-      <param name="" value=""/>
-      <output name="" file=""/>
-    </test>
-  </tests>
--->
-    <configfiles>
-        <configfile name="script_file">
-
-## Feature Selection ##
-get_features &lt;- function(myGenes, f="gene") {
-	if (f == "isoforms")
-		return(isoforms(myGenes))
-	else if (f == "tss")
-		return(TSS(myGenes))
-	else if (f == "cds")
-		return(CDS(myGenes))
-	else
-		return(myGenes)
-}
-
-## Main Function ##
-
-## Load cummeRbund library
-library("cummeRbund")
-
-## Initialize cuff object
-cuff &lt;- readCufflinks(dir = "",
-#if $backend_database_source.backend_database_selector == "cuffdiff_output":
-                         dbFile = "${output_database}",
-                         geneFPKM = "${genes_fpkm_tracking}",
-                         geneDiff = "${genes_exp}",
-                         isoformFPKM = "${isoforms_fpkm_tracking}",
-                         isoformDiff = "${isoforms_exp}",
-                         TSSFPKM = "${tss_groups_fpkm_tracking}",
-                         TSSDiff = "${tss_groups_exp}",
-                         CDSFPKM = "${cds_fpkm_tracking}",
-                         CDSExpDiff = "${cds_exp_diff}",
-                         CDSDiff = "${cds_diff}",
-                         promoterFile = "${promoters_diff}",
-                         splicingFile = "${splicing_diff}",
-                         rebuild = T)
-#else:
-                         dbFile = "${backend_database_source.input_database}",
-                         rebuild = F)
-#end if
-
-#for $i, $p in enumerate($plots, start=1):
-	#set $filename = "plot%02d-%s.png" % ($i, $p.plot['type'])
-png(filename = "${filename}", width = ${p.width}, height = ${p.height})
-
-    ## Density plot ##
-	#if $p.plot['type'] == "density":
-csDensity(genes(cuff))
-devname = dev.off()
-
-    ## Boxplot ##
-	#elif $p.plot['type'] == "boxplot":
-csBoxplot(genes(cuff))
-devname = dev.off()
-
-    ## Scatter ##
-	#elif $p.plot['type'] == "scatter":
-        #if $p.plot.multiple_genes['multiple_genes_selector']:
-myGeneIds &lt;- c()
-            #for $g in $p.plot.multiple_genes['genes']:
-myGeneIds &lt;- c(myGeneIds, "$g['gene_id']")
-            #end for
-myGenes &lt;- getGenes(cuff, myGeneIds)
-csScatter(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth})
-        #else
-csScatter(genes(cuff), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth})
-        #end if
-devname = dev.off()
-
-    ## Volcano ##
-	#elif $p.plot['type'] == "volcano":
-        #if $p.plot.multiple_genes['multiple_genes_selector']:
-myGeneIds &lt;- c()
-            #for $g in $p.plot.multiple_genes['genes']:
-myGeneIds &lt;- c(myGeneIds, "$g['gene_id']")
-            #end for
-myGenes &lt;- getGenes(cuff, myGeneIds)
-csVolcano(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}")
-        #else
-csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}")
-        #end if
-devname = dev.off()
-
-    ## Heatmap ##
-	#elif $p.plot['type'] == "heatmap":
-myGeneIds &lt;- c()
-		#for $g in $p.plot.genes:
-myGeneIds &lt;- c(myGeneIds, "$g['gene_id']")
-		#end for
-myGenes &lt;- getGenes(cuff, myGeneIds)
-csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}")
-devname = dev.off()
-
-    ## Cluster ##
-	#elif $p.plot['type'] == "cluster":
-myGeneIds &lt;- c()
-    	#for $g in $p.plot.genes:
-myGeneIds &lt;- c(myGeneIds, "$g['gene_id']")
-		#end for
-myGenes &lt;- getGenes(cuff, myGeneIds)
-csCluster(get_features(myGenes, "${p.plot.features}"), k=${p.plot.k}, iter.max="${p.plot.iter_max}")
-devname = dev.off()
-
-    ## Expression Plot ##
-	#elif $p.plot['type'] == "expressionplot":
-myGeneId &lt;- "$p.plot.gene_id"
-myGenes &lt;- getGenes(cuff, myGeneId)
-expressionPlot(get_features(myGenes, "${p.plot.features}"), drawSummary=${p.plot.draw_summary}, iter.max="${p.plot.show_error_bars}")
-devname = dev.off()
-
-    ## Expression Bar Plot ##
-	#elif $p.plot['type'] == "expressionbarplot":
-myGeneId &lt;- "$p.plot.gene_id"
-myGenes &lt;- getGenes(cuff, myGeneId)
-expressionBarplot(get_features(myGenes, "${p.plot.features}"), iter.max="${p.plot.show_error_bars}")
-devname = dev.off()
-	#end if
-
-#end for
-        </configfile>
-    </configfiles>
-
-  <help>
-This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
-  </help>
-
-</tool>