diff macs2_bdgcmp.xml @ 0:9c157b556c33 draft

Uploaded

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+++ b/macs2_bdgcmp.xml	Thu Jan 16 13:31:17 2014 -0500
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+<tool id="macs2_bdgcmp" name="Deduct noise" version="2.0.10.0">
+    <description>by comparing two signal tracks in bedGraph (bdgcmp)</description>
+    <requirements>
+        <requirement type="python-module">macs2</requirement>
+        <requirement type="python-module">numpy</requirement>
+        <requirement type="package" version="2.0.10.2">macs2</requirement>
+        <requirement type="package" version="1.7.1">numpy</requirement>
+    </requirements>
+    <command>
+        macs2 bdgcmp
+            -t $input_treatment_file
+            -c $input_control_file
+
+            -m $bdgcmp_options.bdgcmp_options_selector
+            #if $bdgcmp_options.bdgcmp_options_selector in ['FE', 'logFR', 'logLR']:
+                -p $pseudocount
+            #end if
+            --ofile $ofile
+
+    </command>
+    <inputs>
+    <!--experiment name and option of selecting paired or single end will always be present-->
+    <param name="experiment_name" type="text" value="MACS2 in Galaxy" size="50" label="Experiment Name"/>
+
+        <param name="input_treatment_file" type="data" format="bedgraph" label="Treatment bedGraph file" />
+        <param name="input_control_file" type="data" format="bedgraph" label="Control bedGraph file" />
+
+        <conditional name="bdgcmp_options">
+            <param name="bdgcmp_options_selector" type="select" label="Method to use while calculating a score in any bin by comparing treatment value and control value">
+                <option value="ppois">Poisson Pvalue (-log10 (pvalue) form) using control as lambda and treatment as observation</option>
+                <option value="qpois">q-value through a BH process for poisson pvalues</option>
+                <option value="subtract">subtraction from treatment</option>
+                <option value="logFE">log10 fold enrichment</option>
+                <option value="FE">linear scale fold enrichment</option>
+                <option value="logLR">log10 likelihood between ChIP-enriched model and open chromatin model</option>
+                <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models and open chromatin model</option>
+            </param>
+            <when value="FE">
+                <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. DEFAULT: 0.0, no pseudocount is applied."/>
+            </when>
+            <when value="logLR">
+                <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. DEFAULT: 0.0, no pseudocount is applied."/>
+            </when>
+            <when value="logFE">
+                <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. DEFAULT: 0.0, no pseudocount is applied."/>
+            </when>
+        </conditional>
+
+    </inputs>
+
+    <outputs>
+        <data name="ofile" format="bedgraph" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <!--none yet for macs2-->
+    </tests>
+    <help>
+**What it does**
+
+With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq)
+is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for
+identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of
+binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
+
+View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README
+
+------
+
+**Usage**
+
+**Peak Calling**: Main MACS2 Function to Call peaks from alignment results.
+
+**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph.
+
+
+------
+
+**Citation**
+
+For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
+
+Integration of MACS2 with Galaxy performed by Ziru Zhou ( [e-mail] ). Please send your comments/questions to modENCODE DCC at [e-mail].
+    </help>
+</tool>