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Changeset 18:18a7ae54c2e0 (2013-01-21)

Previous changeset 17:d2319b4df472 (2013-01-21) Next changeset 19:b0cd56b01a7c (2013-01-21)

Commit message:
Uploaded

added:
ranger_wrapper.xml

diff -r d2319b4df472 -r 18a7ae54c2e0 ranger_wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ranger_wrapper.xml Mon Jan 21 14:01:02 2013 -0500

[

b'@@ -0,0 +1,255 @@\n+<tool id="modencode_peakcalling_ranger" name="PeakRanger" version="1.16">\n+ <requirements>\n+ <requirement type="set_environment">SCRIPT_PATH</requirement>\n+ <requirement type="package" version="1.16">peakranger</requirement>\n+ </requirements>\n+ <description>multi-purpose, ultrafast ChIP Seq peak caller</description>\n+ <command interpreter="python">ranger_wrapper.py $options_file $outputs_file \\$SCRIPT_PATH</command>\n+ <inputs>\n+ <param name="experiment_name" type="text" value="PeakRanger in Galaxy" size="50" label="Experiment Name"/> \n+\n+ <conditional name="major_command">\n+ <param name="major_command_selector" type="select" label="Select action to be performed">\n+ <option value="nr">Estimate data quality (nr)</option>\n+ <option value="lc">Calculate library complexity (lc)</option>\n+ <option value="wig">Generate coverage wiggle file (wig)</option>\n+ <option value="wigpe">Generate coverage wiggle file using block models (wigpe)</option>\n+ <option value="ranger">Peak calling for sharp peaks (ranger)</option>\n+ <option value="ccat">Peak calling for broad peaks (ccat)</option>\n+ </param>\n+ <when value="nr">\n+ <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />\n+ <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />\n+\n+ <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>\n+ </when>\n+ <when value="lc">\n+ <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />\n+ </when>\n+ <when value="wig">\n+ <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />\n+\n+ <param name="extension" type="integer" value="200" label="Read extension length" help="default=200 (-l)"/>\n+\n+ <param name="split" truevalue="-s" falsevalue="" type="boolean" checked="False" label="Generate one wig file per chromosome" help="output will be in .zip format (-s)"/>\n+ <param name="strand" truevalue="-x" falsevalue="" type="boolean" checked="False" label="Generate one wig file per strand" help="output will be in .zip format (-x)"/>\n+ <param name="gzip" truevalue="-z" falsevalue="" type="boolean" checked="False" label="Compress the output" help="(-z)"/>\n+ </when>\n+ <when value="wigpe">\n+ <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />\n+\n+ <param name="extension" type="integer" value="0" label="Read extension length" help="default=0 (-l)"/>\n+\n+ <param name="split" truevalue="-s" falsevalue="" type="boolean" checked="False" label="Generate one wig file per chromosome" help="(-s)"/>\n+ <param name="strand" truevalue="-x" falsevalue="" type="boolean" checked="False" label="Generate one wig file per strand" help="(-x)"/>\n+ <param name="gzip" truevalue="-z" falsevalue="" type="boolean" checked="False" label="Compress the output" help="(-z)"/>\n+ </when>\n+ <when value="ranger">\n+ <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" />\n+ <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Control File" />\n+\n+ <conditional name="gene_annotate_file">\n+ <param name="gene_annotate_file_selector" type="select" label="Select the gene annotation file">\n+ <option value="dm3refGene.txt">dm3refGene.txt</option>\n+ <option value="hg19refGene.txt">hg19refGene.txt</option>\n+ <option value="mm9refGene.txt">mm9refGene.txt</option>\n+ <option value="Upload">Select from history</option>\n+ <option value="None">None</option>\n+ </param>\n+ <when value="upload">\n+ <p'..b"$major_command.input_control_file1 )\n+\n+ #set $__options['gene_annotate_file'] = str( $major_command.gene_annotate_file.gene_annotate_file_selector )\n+ #if str( $major_command.gene_annotate_file.gene_annotate_file_selector ) == 'Upload'\n+ #set $__options['usr_annot_file'] = str( $major_command.gene_annotate_file.usr_annot_file ) \n+ #end if\n+\n+ #set $__options['plot_region'] = str( $major_command.plot_region )\n+ #set $__options['pvalue'] = str( $major_command.pvalue )\n+ #set $__options['fdr'] = str( $major_command.fdr )\n+ #set $__options['extension'] = str( $major_command.extension )\n+ #set $__options['delta'] = str( $major_command.delta )\n+ #set $__options['threads'] = str( $major_command.threads )\n+ #set $__options['bandwith'] = str( $major_command.bandwith )\n+ #set $__options['pad'] = str( $major_command.pad )\n+#end if\n+##=============================================================================\n+#if str($major_command.major_command_selector) == 'ccat':\n+ #set $__options['chip_file'] = str( $major_command.input_chipseq_file1 )\n+ #set $__options['input_file'] = str( $major_command.input_control_file1 )\n+\n+ #set $__options['gene_annotate_file'] = str( $major_command.gene_annotate_file.gene_annotate_file_selector )\n+ #if str( $major_command.gene_annotate_file.gene_annotate_file_selector ) == 'Upload'\n+ #set $__options['usr_annot_file'] = str( $major_command.gene_annotate_file.usr_annot_file ) \n+ #end if\n+\n+ #set $__options['plot_region'] = str( $major_command.plot_region )\n+ #set $__options['fdr'] = str( $major_command.fdr )\n+ #set $__options['extension'] = str( $major_command.extension )\n+ #set $__options['winsize'] = str( $major_command.winsize )\n+ #set $__options['winstep'] = str( $major_command.winstep )\n+ #set $__options['mincount'] = str( $major_command.mincount )\n+ #set $__options['minscore'] = str( $major_command.minscore )\n+#end if\n+##=============================================================================\n+${ simplejson.dumps( __options ) }\n+ </configfile>\n+ </configfiles>\n+ <tests>\n+ \n+ </tests>\n+ <help>\n+**What it does**\n+\n+PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data. The suite contains the following tools:\n+\n+View the modified PeakRanger documentation: http://ranger.sourceforge.net/manualv116.html#introduction\n+\n+------\n+\n+**Usage**\n+\n+**nr:** noise rate estimator. Estimates signal to noise ratio which is an indicator for ChIP enrichment\n+\n+**lc:** library complexity calculator. Calculates the ratio of unique reads over total reads. Only accepts bam files.\n+\n+**wig:** coverage file generator. Generates variable step format wiggle file\n+\n+**wigpe:** coverage file generator. Generates bedGraph format wiggle file and supports spliced alignments and thus only supports bam files\n+\n+ wigpe can also generate coverage files for bam files containing spliced reads, such as those from RNA-Seq experiments.\n+\n+**ranger:** ChIP-Seq peak caller. It is able to identify enriched genomic regions while at the same time discover summits within these regions.\n+\n+**ccat:** ChIP-Seq peak caller. Tuned for the discovery of broad peaks\n+\n+ Both ranger and ccat supports generating HTML-based annotation reports.\n+\n+------\n+\n+**Citation**\n+\n+If you use PeakRanger in your research, please cite:\n+Feng X, Grossman R, Stein L: PeakRanger:A cloud-enabled peak caller for ChIP-seq data.BMC Bioinformatics 2011, 12(1):139.\n+\n+if you use the ccat tool, please also cite:\n+Xu, H., L. Handoko, et al. (2010).A signal-noise model for significance analysis of ChIP-seq with negative control.Bioinformatics 26(9): 1199-1204.\n+\n+\n+Integration of PeakRanger with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to help@modencode.org.\n+ </help>\n+</tool>\n\\ No newline at end of file\n"