view foldchanges_heatmap.xml @ 21:d32de046ba31 draft

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<tool id="foldchange_heatmap" name="fold change heatmap" version="1.0">
    <description>Plot heat map of fold changes from multiple DESeq2 outputs</description>
    <requirements>
        <requirement type="binary">Rscript</requirement>
        <requirement type="package" version="3.0.2">R_3_0_2</requirement>
    </requirements>
    <command interpreter="Rscript">
            #set $label_list = list()
            #set $table_list = list()
            #for $input in $deseqout:
                $label_list.append('%s' %($input.label))
            #end for
            #for $input in $deseqout:
                $table_list.append('%s' %($input.table))
            #end for
            foldchanges_heatmap.r "#echo ','.join( $label_list )#" "#echo ','.join( $table_list )#" $gene_ids_file $plots
            ## TODO: instead of throwing away stderr, try Bjoern's fix
            2> /dev/null
    </command>
    <stdio>
        <regex match="Execution halted" 
           source="both" 
           level="fatal" 
           description="Execution halted." />
    </stdio>
    <inputs>
        <repeat name="deseqout" title="DESeq2 output" min="1">
            <param name="label" type="text" value="Label" label="Specify a label" help="" />
            <param name="table" label="Select DESeq2 output" type="data" format="tabular"/>
        </repeat>
        <param name="gene_ids_file" label="Select file containing gene ids" type="data" format="tabular"/>
    </inputs>

    <outputs>
        <data format="pdf" name="plots" label="Heatmap plot on ${on_string}"/>
    </outputs>
    <help>

.. class:: infomark

**What it does** 

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution


**Inputs**

DESeq2_ requires one count matrix as input file. You can use the tool



**Output**

DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.

====== ==========================================================
Column Description
------ ----------------------------------------------------------
     1 Gene Identifiers
     2 mean normalised counts, averaged over all samples from both conditions
     3 the logarithm (to basis 2) of the fold change
     4 standard error estimate for the log2 fold change estimate
     5 p value for the statistical significance of this change
     6 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
       which controls false discovery rate (FDR)
====== ==========================================================


------

**References** 

DESeq2_ Authors: Michael Love (MPIMG Berlin), Simon Anders, Wolfgang Huber (EMBL Heidelberg)

If DESeq2_ is used to obtain results for scientific publications it
should be cited as [1]_. A paper describing DESeq2_ is in preparation.



.. [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`_. 

.. _Differential expression analysis for sequence count data: http://dx.doi.org/10.1186/gb-2010-11-10-r106
.. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html


    </help>
</tool>