comparison limma_voom.xml @ 3:38aab66ae5cb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65

2:a330ddf43861

<tool id="limma_voom" name="limma-voom" version="1.2.0">
    <description>
        Differential expression with optional sample weights
    </description>

    <requirements>
        <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
        <requirement type="package" version="3.30.13">bioconductor-limma</requirement>
        <requirement type="package" version="1.4.29">r-statmod</requirement>
        <requirement type="package" version="0.4.1">r-scales</requirement>
    </requirements>

    <version_command><![CDATA[
        echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>

    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/limma_voom.R'
'$counts'

#if $anno.annoOpt=='yes':
  '$geneanno'
#else:
  None
#end if

'$outReport'
'$outReport.files_path'
$rdaOption
$normalisationOption
$weightOption
'$contrast'

#if $filterCPM.filterLowCPM=='yes':
  '$filterCPM.cpmReq'
  '$filterCPM.sampleReq'
#else:
  0
  0
#end if

#if $testOpt.wantOpt=='yes':
  '$testOpt.pAdjust'
  '$testOpt.pVal'
  '$testOpt.lfc'
#else:
  "BH"
  0.05
  0
#end if

$normCounts

#if $fact.ffile=='yes':
    '$finfo'
    'None'
#else:
    'None'
    '$fact.pfactName::$fact.pfactLevel'
    #for $sfact in $fact.sfactors:
        '$sfact.sfactName::$sfact.sfactLevel'
    #end for
#end if

&&
mkdir ./output_dir

&&
cp '$outReport.files_path'/*.tsv output_dir/
    ]]></command>

    <inputs>
        <param name="counts" type="data" format="tabular" label="Counts Data"/>

        <conditional name="anno">
            <param name="annoOpt" type="select" label="Use Gene Annotations?"
                help="If an annotation file is provided, annotations will be added to the table of differential expression results to provide descriptions for each gene.">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
            </when>
            <when value="no" />
        </conditional>

        <conditional name="fact">
            <param name="ffile" type="select" label="Input Factor Information from file?"
                help="You can choose to input the factor information from a file or manually enter below.">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="finfo" type="data" format="tabular" label="Factor Information"/>
            </when>
            <when value="no" >
                <param name="pfactName" type="text" label="Primary Factor Name"
                    help="Eg. Genotype NOTE: Please only use letters, numbers or underscores.">
                    <validator type="empty_field" />
                    <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
                </param>
                <param name="pfactLevel" type="text" label="Primary Factor Levels"
                    help="Eg. WT,WT,WT,Mut,Mut,Mut NOTE: Please only use letters, numbers or underscores and ensure that the same levels are typed identically with cases matching.">
                    <validator type="empty_field" />
                    <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
                </param>
                <repeat name="sfactors" title="Secondary Factor" >
                    <param name="sfactName" type="text" label="Secondary Factor Name" help="Eg. Batch">
                        <validator type="empty_field" />
                        <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
                    </param>
                    <param name="sfactLevel" type="text" label="Secondary Factor Levels"
                        help="Eg. b1,b2,b3,b1,b2,b3 NOTE: Please only use letters, numbers or underscores and ensure that the same levels are typed identically with cases matching.">
                        <validator type="empty_field" />
                        <validator type="regex" message="Please only use letters, numbers or underscores">^[\w,]+$</validator>
                    </param>
                </repeat>
            </when>
        </conditional>

        <param name="contrast" type="text" label="Contrasts of interest" help="Eg. Mut-WT,KD-Control">
            <validator type="empty_field" />
            <validator type="regex" message="Please only use letters, numbers or underscores">^[\w,-]+$</validator>
        </param>

        <conditional name="filterCPM">
            <param name="filterLowCPM" type="select" label="Filter Low CPM?"
                help="Treat genes with very low expression as unexpressed and filter out to speed up computation.">
                <option value="yes" selected="True">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="yes">
                <param name="cpmReq" type="float" value="0.5" min="0" label="Minimum CPM"/>
                <param name="sampleReq" type="integer" value="1" min="0" label="Minimum Samples"
                    help="Filter out all the genes that do not meet the minimum CPM in at least this many samples."/>
            </when>
            <when value="no"/>
        </conditional>

        <param name="weightOption" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Apply sample weights?"
            help="Apply weights if outliers are present.">
        </param>

        <param name="normalisationOption" type="select" label="Normalisation Method">
            <option value="TMM">TMM</option>
            <option value="RLE">RLE</option>
            <option value="upperquartile">Upperquartile</option>
            <option value="none">None (Don't normalise)</option>
        </param>

        <param name="normCounts" type="boolean" truevalue="yes" falsevalue="no" checked="false"
            label="Output normalised counts table?"
            help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM).">
        </param>

        <param name="rdaOption" type="boolean" truevalue="yes" falsevalue="no" checked="false"
            label="Output RData?"
            help="Output all the data used by R to construct the plots and tables, can be loaded into R. A link to the RData file will be provided in the HTML report.">
        </param>

        <conditional name="testOpt">
            <param name="wantOpt" type="select" label="Use Advanced Testing Options?"
                help="Enable choices for p-value adjustment method, p-value threshold and log2-fold-change threshold.">
                <option value="no" selected="True">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="pAdjust" type="select" label="P-Value Adjustment Method.">
                    <option value="BH">Benjamini and Hochberg (1995)</option>
                    <option value="BY">Benjamini and Yekutieli (2001)</option>
                    <option value="holm">Holm (1979)</option>
                    <option value="none">None</option>
                </param>
                <param name="pVal" type="float" value="0.05" min="0" max="1"
                    label="Adjusted Threshold"
                    help="Genes below this threshold are considered significant and highlighted in the MA plot. If either BH(1995) or BY(2001) were selected then this value is a false-discovery-rate control. If Holm(1979) was selected then this is an adjusted p-value for family-wise error rate."/>
                <param name="lfc" type="float" value="0" min="0"
                    label="Minimum log2-fold-change Required"
                    help="Genes above this threshold and below the p-value threshold are considered significant and highlighted in the MA plot."/>
            </when>
            <when value="no"/>
        </conditional>

    </inputs>

    <outputs>
        <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />

            <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
        </collection>
    </outputs>

    <tests>
        <test>
            <param name="counts" value="matrix.txt" />
            <param name="pfactName" value="Genotype" />
            <param name="pfactLevel" value="WT,WT,WT,Mut,Mut,Mut" />
            <param name="contrast" value="Mut-WT,WT-Mut" />
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="2">
                <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT.tsv" />
                <element name="limma-voom_WT-Mut" ftype="tabular" file="limma-voom_WT-Mut.tsv" />
            </output_collection>
            <output name="outReport" >
                <assert_contents>
                    <has_text text="Limma-voom Analysis Output" />
                    <not_has_text text="RData" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="annoOpt" value="yes" />
            <param name="geneanno" value="anno.txt" />
            <param name="counts" value="matrix.txt" />
            <param name="pfactName" value="Genotype" />
            <param name="pfactLevel" value="WT,WT,WT,Mut,Mut,Mut" />
            <param name="contrast" value="Mut-WT" />
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" >
                <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WTanno.tsv" />
            </output_collection>
        </test>
        <test>
            <param name="rdaOption" value="yes" />
            <param name="counts" value="matrix.txt" />
            <param name="pfactName" value="Genotype" />
            <param name="pfactLevel" value="WT,WT,WT,Mut,Mut,Mut" />
            <param name="contrast" value="Mut-WT" />
            <param name="normalisationOption" value="TMM" />
            <output name="outReport" >
                <assert_contents>
                    <has_text text="RData" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="counts" value="matrix.txt" />
            <param name="pfactName" value="Genotype"/>
            <param name="pfactLevel" value="WT,WT,WT,Mut,Mut,Mut"/>
            <repeat name="sfactors">
                <param name="sfactName" value="Batch"/>
                <param name="sfactLevel" value="b1,b2,b3,b1,b2,b3"/>
            </repeat>
            <param name="contrast" value="Mut-WT" />
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" >
                <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WTmultifact.tsv" />
            </output_collection>
        </test>
        <test>
            <param name="ffile" value="yes" />
            <param name="finfo" value="factorinfo.txt" />
            <param name="counts" value="matrix.txt" />
            <param name="contrast" value="Mut-WT" />
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" >
                <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WTmultifact.tsv" />
            </output_collection>
        </test>
        <test>
            <param name="normCounts" value="yes" />
            <param name="counts" value="matrix.txt" />
            <param name="pfactName" value="Genotype" />
            <param name="pfactLevel" value="WT,WT,WT,Mut,Mut,Mut" />
            <param name="contrast" value="Mut-WT" />
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="2">
                <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT.tsv" />
                <element name="limma-voom_normcounts" ftype="tabular" file="limma-voom_normcounts.tsv" />
            </output_collection>
        </test>
    </tests>

    <help><![CDATA[
.. class:: infomark

**What it does**

Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, this tool
produces plots and tables useful in the analysis of differential gene
expression.

-----

**Inputs**

**Counts Data:**
A matrix of counts, with rows corresponding to genes
and columns corresponding to counts for the samples.
Values must be tab separated, with the first row containing the sample/column
labels and the first column containing the row/gene labels.

Example:

    ========== ======= ======= ======= ======== ======== ========
    **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3**
    ---------- ------- ------- ------- -------- -------- --------
    11287      1699    1528    1601    1463     1441     1495

    1304        Abca4       ATP-binding cassette, sub-family A (ABC1), member 4
    1305        Abca2       ATP-binding cassette, sub-family A (ABC1), member 2
    ==========  ==========  ===================================================

**Factor Information:**
Enter Factor Names and Levels in the tool form or provide a tab-separated file that has the samples in the same order as listed in the columns of the counts matrix. The second column should contain the Primary Factor levels (e.g. Genotype) with optional additional columns for any Secondary Factors (e.g. Batch).

Example:

    ========== ============ =========
    **Sample** **Genotype** **Batch**

    Mut1       Mut          b1
    Mut2       Mut          b2
    Mut3       Mut          b3
    ========== ============ =========

**Primary Factor Name:** The name of the primary factor being investigated e.g. Genotype. One primary factor must be entered and spaces must not be used.

**Primary Factor Levels:** The levels of the primary factor of interest, these must be entered in the same order as the samples to which the levels correspond, as listed in the columns of the counts matrix. Spaces must not be used and if entered in the tool form the values should be separated by commas.

**Secondary Factor Name:** Optionally, one or more secondary factors can be included. These are variables that might influence your experiment e.g. Batch, Gender. Spaces must not be used.

**Secondary Factor Levels:** The levels of the secondary factor of interest, these must be entered in the same order as the samples to which the levels correspond, as listed in the columns of the counts matrix. Spaces must not be used and if entered in the tool form the values should be separated by commas.


**Contrasts of Interest:**
The contrasts you wish to make between levels.
A common contrast would be a simple difference between two levels: "Mut-WT"
represents the difference between the mutant and wild type genotypes.
Multiple contrasts should be separated by commas and spaces must not be used.

**Filter Low CPM:**
Option to ignore the genes that do not show significant levels of
expression, this filtering is dependent on two criteria:

    * **Minimum CPM:** This is the counts per million that a gene must have in at
      least some specified number of samples.

    * **Minumum Samples:** This is the number of samples in which the CPM
      requirement must be met in order for that gene to be acknowledged.

Only genes that exhibit a CPM greater than the required amount in at least the
number of samples specified will be used for analysis. Care should be taken to
ensure that the sample requirement is appropriate. In the case of an experiment
with two experimental groups each with two members, if there is a change from
insignificant cpm to significant cpm but the sample requirement is set to 3,
then this will cause that gene to fail the criteria. When in doubt simply do not
filter.

**Normalisation Method:**
Option for using different methods to rescale the raw library
size. For more information, see calcNormFactor section in the edgeR_ user's
manual.

**Apply Sample Weights:**
Option to downweight outlier samples such that their information is still
used in the statistical analysis but their impact is reduced. Use this
whenever significant outliers are present. The MDS plotting tool in this package
is useful for identifying outliers. For more information on this option see Liu et al. (2015).

**Use Advanced Testing Options?:**
By default error rate for multiple testing is controlled using Benjamini and
Hochberg's false discovery rate control at a threshold value of 0.05. However
there are options to change this to custom values.

    * **P-Value Adjustment Method:**
      Change the multiple testing control method, the options are BH(1995) and
      BY(2001) which are both false discovery rate controls. There is also
      Holm(1979) which is a method for family-wise error rate control.

    * **Adjusted Threshold:**
      Set the threshold for the resulting value of the multiple testing control
      method. Only observations whose statistic falls below this value is
      considered significant, thus highlighted in the MA plot.

    * **Minimum log2-fold-change Required:**
      In addition to meeting the requirement for the adjusted statistic for
      multiple testing, the observation must have an absolute log2-fold-change
      greater than this threshold to be considered significant, thus highlighted
      in the MA plot.

**Outputs**

This tool outputs a table of differentially expressed genes for each contrast of interest and a HTML report with plots and additional information. Optionally you can choose to output the normalised counts table and the RData file.

-----

**Citations:**

.. class:: infomark

limma

Please cite the paper below for the limma software itself. Please also try
to cite the appropriate methodology articles that describe the statistical
methods implemented in limma, depending on which limma functions you are
using.  The methodology articles are listed in Section 2.1 of the limma
User's Guide.

    * Smyth GK (2005). Limma: linear models for microarray data. In:
      'Bioinformatics and Computational Biology Solutions using R and
      Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry,
      W. Huber (eds), Springer, New York, pages 397-420.

    * Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic,
      A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights
      for microarray data. BMC Bioinformatics 7, Article 261.

.. class:: infomark

edgeR

Please cite the first paper for the software itself and the other papers for
the various original statistical methods implemented in edgeR.  See
Section 1.2 in the User's Guide for more detail.

    * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor
      package for differential expression analysis of digital gene expression
      data. Bioinformatics 26, 139-140

      of multifactor RNA-Seq experiments with respect to biological variation.
      Nucleic Acids Research 40, 4288-4297

Please report problems or suggestions to: [e-mail]

.. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
.. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html
    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gkv412</citation>
    </citations>
</tool>

3:38aab66ae5cb

<tool id="limma_voom" name="limma" version="3.34.6.0">
    <description>
        Perform differential expression with limma-voom or limma-trend
    </description>

    <requirements>
        <requirement type="package" version="3.34.6">bioconductor-limma</requirement>
        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
        <requirement type="package" version="1.4.30">r-statmod</requirement>
        <requirement type="package" version="0.5.0">r-scales</requirement>
        <requirement type="package" version="0.2.15">r-rjson</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
    </requirements>

    <version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>

    <command detect_errors="exit_code"><![CDATA[
#import json
Rscript '$__tool_directory__/limma_voom.R'

-R '$outReport'
-o '$outReport.files_path'

#if $input.format=="files":

    ## Adapted from DESeq2 wrapper
    #set $temp_factor_names = list()
    #for $fact in $input.rep_factor:
        #set $temp_factor = list()
        #for $g in $fact.rep_group:
            #set $count_files = list()
            #for $file in $g.countsFile:
                $count_files.append(str($file))
            #end for
            $temp_factor.append( {str($g.groupName): $count_files} )
        #end for

        $temp_factor.reverse()
        $temp_factor_names.append([str($fact.factorName), $temp_factor])
    #end for
    -j '#echo json.dumps(temp_factor_names)#'

#elif $input.format=="matrix":
    -m '$input.counts'
    #if $input.fact.ffile=='yes':
        -f '$input.fact.finfo'
    #else:
        -i '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
    #end if
#end if

#if $anno.annoOpt=='yes':
    -a '$anno.geneanno'
#end if

-C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }'

#if $f.filt.filt_select == 'yes':
    #if $f.filt.cformat.format_select == 'cpm':
        -c '$f.filt.cformat.cpmReq'
        -s '$f.filt.cformat.cpmSampleReq'
    #elif $f.filt.cformat.format_select == 'counts':
            -z '$f.filt.cformat.cntReq'
        #if $f.filt.cformat.samples.count_select == 'total':
            -y
        #elif $f.filt.cformat.samples.count_select == 'sample':
            -s '$f.filt.cformat.samples.cntSampleReq'
        #end if
    #end if
#end if

#if $out.normCounts:
    -x
#end if

#if $out.rdaOption:
    -r
#end if

-l '$adv.lfc'
-p '$adv.pVal'
-d '$adv.pAdjust'

#if $deMethod.de_select == 'voom':
    #if $deMethod.weightOption:
        -w
    #end if
#elif $deMethod.de_select == 'trend':
    -t $deMethod.prior_count
#end if

-n '$adv.normalisationOption'

#if $adv.robOption:
    -b
#end if

&&
mkdir ./output_dir

&&
cp '$outReport.files_path'/*.tsv output_dir/
    ]]></command>

    <inputs>

        <!-- DE Method Option -->
        <conditional name="deMethod">
            <param name="de_select" type="select" label="Differential Expression Method" help="Select the limma-voom or limma-trend method. See Help section below for more information. Default: limma-voom">
                <option value="voom" selected="True">limma-voom</option>
                <option value="trend">limma-trend</option>
            </param>
            <when value="voom">
                <param name="weightOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Apply voom with sample quality weights?"
                help="Apply weights if outliers are present (voomWithQualityWeights). Default: False.">
                </param>
            </when>
            <when value="trend">
                <param name="prior_count" type="float" min="0" value="3" label="Prior count" help="Average count to be added to each observation to avoid taking log of zero. Default: 3." />
            </when>
        </conditional>
        <!-- Counts and Factors -->
        <conditional name="input">
            <param name="format" type="select" label="Count Files or Matrix?"
                help="You can choose to input either separate count files (one per sample) or a single count matrix">
                <option value="files">Separate Count Files</option>
                <option value="matrix">Single Count Matrix</option>
            </param>

            <when value="files">
                <repeat name="rep_factor" title="Factor" min="1">
                    <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores.">
                    <sanitizer>
                        <valid initial="string.letters,string.digits"><add value="_" /></valid>
                    </sanitizer>
                    </param>
                    <repeat name="rep_group" title="Group" min="2" default="2">
                        <param name="groupName" type="text" label="Name"
                        help="Name of group that the counts files(s) belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive).">
                        <sanitizer>
                            <valid initial="string.letters,string.digits"><add value="_" /></valid>
                        </sanitizer>
                        </param>
                        <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
                    </repeat>
                </repeat>
            </when>

            <when value="matrix">
                <param name="counts" type="data" format="tabular" label="Count Matrix"/>

                <conditional name="fact">
                    <param name="ffile" type="select" label="Input factor information from file?"
                        help="You can choose to input the factor and group information for the samples from a file or manually enter below.">
                        <option value="no">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="yes">
                        <param name="finfo" type="data" format="tabular" label="Factor File"/>
                    </when>
                    <when value="no" >
                        <repeat name="rep_factor" title="Factor" min="1">
                            <param name="factorName" type="text" label="Factor Name"
                                help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores.">
                                <validator type="empty_field" />
                                <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
                            </param>
                            <param name="groupNames" type="text" label="Groups"
                                help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive).">
                                <validator type="empty_field" />
                                <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
                            </param>
                        </repeat>
                    </when>
                </conditional>
            </when>
        </conditional>

        <!-- Gene Annotations -->
        <conditional name="anno">
            <param name="annoOpt" type="select" label="Use Gene Annotations?"
                    help="If you provide an annotation file, annotations will be added to the table(s) of differential expression results to provide descriptions for each gene. See Help section below.">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
            </when>
            <when value="no" />
        </conditional>

        <!-- Contrasts -->
        <repeat name="rep_contrast" title="Contrast" min="1" default="1">
            <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
                <validator type="empty_field" />
                <validator type="regex" message="Please only use letters, numbers or underscores">^[\w-]+$</validator>
            </param>
        </repeat>

        <!-- Filter Options -->
        <section name="f" expanded="false" title="Filter Low Counts">
            <conditional name="filt">
                <param name="filt_select" type="select" label="Filter lowly expressed genes?" help="Treat genes with very low expression as unexpressed and filter out. See the Filter Low Counts section below for more information. Default: No">
                    <option value="no" selected="true">No</option>
                    <option value="yes">Yes</option>
                </param>
                <when value="yes">
                    <conditional name="cformat">
                        <param name="format_select" type="select" label="Filter on CPM or Count values?" help="It is slightly better to base the filtering on count-per-million (CPM) rather than the raw count values so as to avoid favoring genes expressed in samples sequenced to a higher depth. ">
                            <option value="cpm">CPM</option>
                            <option value="counts">Counts</option>
                        </param>
                        <when value="cpm">
                            <param name="cpmReq" type="float" value="1" min="0" label="Minimum CPM" help="Treat genes with CPM below this value as unexpressed and filter out. See the Filter Low Counts section below for more information."/>
                             <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
                             help="Filter out all genes that do not meet the Minimum CPM in at least this many samples. See the Filter Low Counts section below for more information."/>
                        </when>
                        <when value="counts">
                            <param name="cntReq" type="integer" value="0" min="0" label="Minimum Count" help="Filter out all genes that do not meet this minimum count. You can choose below to apply this filter to the total count for all samples or specify the number of samples under Minimum Samples. See the Filter Low Counts section below for more information." />
                            <conditional name="samples">
                                <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" >
                                    <option value="total">Total</option>
                                    <option value="sample">Sample</option>
                                </param>
                                <when value="total">
                                    <param name="totReq" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Filter on Total Count" help="Apply the Minimum Count filter to genes after summing counts for all samples. See the Filter Low Counts section below for more information." />
                                </when>
                                <when value="sample">
                                    <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
                                    help="Filter out all genes that do not meet the Minimum Count in at least this many samples. See the Filter Low Counts section below for more information."/>
                                </when>
                            </conditional>
                        </when>
                    </conditional>
                </when>
                <when value="no" />
            </conditional>
        </section>

        <!-- Output Options -->
        <section name="out" expanded="false" title="Output Options">
            <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
                label="Output Normalised Counts Table?"
                help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
            </param>
            <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
                label="Output RData file?"
                help="Output all the data used by R to construct the plots and tables, can be loaded into R. A link to the RData file will be provided in the HTML report. Default: No">
            </param>
        </section>

        <!-- Advanced Options -->
        <section name="adv" expanded="false" title="Advanced Options">
            <param name="lfc" type="float" value="0" min="0"
                label="Minimum Log2 Fold Change"
                help="Genes above this threshold and below the p-value threshold are considered significant and highlighted in the MD plot. Default: 0."/>
            <param name="pVal" type="float" value="0.05" min="0" max="1"
                label="P-Value Adjusted Threshold"
                help="Genes below this threshold are considered significant and highlighted in the MD plot. If either BH(1995) or BY(2001) are selected then this value is a false-discovery-rate control. If Holm(1979) is selected then this is an adjusted p-value for family-wise error rate. Default: 0.05."/>
            <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH">
                <option value="BH" selected="true">Benjamini and Hochberg (1995)</option>
                <option value="BY">Benjamini and Yekutieli (2001)</option>
                <option value="holm">Holm (1979)</option>
                <option value="none">None</option>
            </param>
            <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
                <option value="TMM" selected="true">TMM</option>
                <option value="RLE">RLE</option>
                <option value="upperquartile">Upperquartile</option>
                <option value="none">None (Don't normalise)</option>
            </param>
            <param name="robOption" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use Robust Settings?" help="Using robust settings is usually recommended to protect against outlier genes. Default: Yes" />
        </section>

    </inputs>

    <outputs>
        <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />

            <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
        </collection>
    </outputs>

    <tests>
        <!-- Ensure report is output -->
        <test>
            <param name="format" value="matrix" />
            <param name="counts" value="matrix.txt" />
            <repeat name="rep_factor">
                <param name="factorName" value="Genotype"/>
                <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="WT-Mut" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="2">
                <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT.tsv" />
                <element name="limma-voom_WT-Mut" ftype="tabular" file="limma-voom_WT-Mut.tsv" />
            </output_collection>
            <output name="outReport" >
                <assert_contents>
                    <has_text text="Limma Analysis Output" />
                    <not_has_text text="RData" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure annotation file input works -->
        <test>
            <param name="format" value="matrix" />
            <param name="annoOpt" value="yes" />
            <param name="geneanno" value="anno.txt" />
            <param name="counts" value="matrix.txt" />
            <repeat name="rep_factor">
                <param name="factorName" value="Genotype"/>
                <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="1">
                <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT_anno.tsv" />
            </output_collection>
        </test>
        <!-- Ensure RData file can be output -->
        <test>
            <param name="format" value="matrix" />
            <param name="rdaOption" value="true" />
            <param name="counts" value="matrix.txt" />
            <repeat name="rep_factor">
                <param name="factorName" value="Genotype"/>
                <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output name="outReport" >
                <assert_contents>
                    <has_text text="RData" />
                </assert_contents>
            </output>
        </test>
        <!-- Ensure secondary factors work -->
        <test>
            <param name="format" value="matrix" />
            <param name="counts" value="matrix.txt" />
            <repeat name="rep_factor">
                <param name="factorName" value="Genotype"/>
                <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
            </repeat>
            <repeat name="rep_factor">
                <param name="factorName" value="Batch"/>
                <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/>
            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="1" >
                <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT_2fact.tsv" />
            </output_collection>
        </test>
        <!-- Ensure factors file input works -->
        <test>
            <param name="format" value="matrix" />
            <param name="ffile" value="yes" />
            <param name="finfo" value="factorinfo.txt" />
            <param name="counts" value="matrix.txt" />
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="1">
                <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT_2fact.tsv" />
            </output_collection>
        </test>
        <!-- Ensure normalised counts file output works-->
        <test>
            <param name="format" value="matrix" />
            <param name="normCounts" value="true" />
            <param name="counts" value="matrix.txt" />
            <repeat name="rep_factor">
                <param name="factorName" value="Genotype"/>
                <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <output_collection name="outTables" count="2">
                <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT.tsv" />
                <element name="limma-voom_normcounts" ftype="tabular" file="limma-voom_normcounts.tsv" />
            </output_collection>
        </test>
        <!-- Ensure multiple counts files input works -->
        <test>
            <param name="format" value="files" />
            <repeat name="rep_factor">
                <param name="factorName" value="Genotype"/>
                <repeat name="rep_group">
                    <param name="groupName" value="WT"/>
                    <param name="countsFile" value="WT1.counts,WT2.counts,WT3.counts"/>
                </repeat>
                <repeat name="rep_group">
                    <param name="groupName" value="Mut"/>
                    <param name="countsFile" value="Mut1.counts,Mut2.counts,Mut3.counts"/>
                </repeat>
            </repeat>
            <repeat name="rep_factor">
                <param name="factorName" value="Batch"/>
                <repeat name="rep_group">
                    <param name="groupName" value="b1"/>
                    <param name="countsFile" value="WT1.counts,Mut1.counts"/>
                </repeat>
                <repeat name="rep_group">
                    <param name="groupName" value="b2"/>
                    <param name="countsFile" value="WT2.counts,Mut2.counts"/>
                </repeat>
                <repeat name="rep_group">
                    <param name="groupName" value="b3"/>
                    <param name="countsFile" value="WT3.counts,Mut3.counts"/>
                </repeat>
            </repeat>
            <param name="annoOpt" value="yes" />
            <param name="geneanno" value="anno.txt" />
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="WT-Mut" />
            </repeat>
            <param name="normCounts" value="true" />
            <output_collection name="outTables" count="3">
                <element name="limma-voom_Mut-WT" ftype="tabular" file="limma-voom_Mut-WT_2fact_anno.tsv" />
                <element name="limma-voom_WT-Mut" ftype="tabular" file="limma-voom_WT-Mut_2fact_anno.tsv" />
                <element name="limma-voom_normcounts" ftype="tabular" file="limma-voom_normcounts_anno.tsv" />
            </output_collection>
        </test>
        <!-- Ensure limma-trend option works -->
        <test>
            <param name="format" value="matrix" />
            <param name="counts" value="matrix.txt" />
            <repeat name="rep_factor">
                <param name="factorName" value="Genotype"/>
                <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
            </repeat>
            <repeat name="rep_contrast">
                <param name="contrast" value="Mut-WT" />
            </repeat>
            <param name="normalisationOption" value="TMM" />
            <param name="de_select" value="trend" />
            <param name="rdaOption" value="true" />
            <output name="outReport" >
                <assert_contents>
                    <has_text text="The limma-trend method was used" />
                </assert_contents>
            </output>
            <output_collection name="outTables" count="1">
                <element name="limma-trend_Mut-WT" ftype="tabular" file="limma-trend_Mut-WT.tsv" />
            </output_collection>
        </test>
    </tests>

    <help><![CDATA[
.. class:: infomark

**What it does**

Given a matrix of counts (e.g. from featureCounts) and optional information about the genes, performs differential expression (DE) using the limma_ Bioconductor package and produces plots and tables useful in DE analysis.

In the `limma approach`_ to RNA-seq, read counts are converted to log2-counts-per-million (logCPM) and the mean-variance relationship is modelled either with precision weights or with an empirical Bayes prior trend. The precision weights approach is called “voom” and the prior trend approach is called “limma-trend”. For more information, see the Help section below.

-----

**Inputs**

**Differential Expression Method:**
Option to use the limma-voom or limma-trend approach for differential expression. The default is limma-voom.
If the sequencing depth is reasonably consistent across the RNA samples, then the simplest and most
robust approach to differential expression is to use limma-trend. This approach will usually work well if the
ratio of the largest library size to the smallest is not more than about 3-fold. When the library sizes are quite variable between samples, then the voom approach is theoretically more powerful than limma-trend. For more information see the excellent `limma User's Guide`_.

**Counts Data:**

The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. Gene identifiers can be of any type but must be unique and not repeated within a counts file.

Example - **Separate Count Files**:

    ========== =======
    **GeneID** **WT1**
    ---------- -------
    11287      1699
    11298      1905
    11302      6
    11303      2099
    11304      356
    11305      2528
    ========== =======

Example - **Single Count Matrix**:

    ========== ======= ======= ======= ======== ======== ========
    **GeneID** **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3**
    ---------- ------- ------- ------- -------- -------- --------
    11287      1699    1528    1601    1463     1441     1495

    1304        Abca4       ATP-binding cassette, sub-family A (ABC1), member 4
    1305        Abca2       ATP-binding cassette, sub-family A (ABC1), member 2
    ==========  ==========  ===================================================

**Factor Information:**
Enter factor names and groups in the tool form, or provide a tab-separated file that has the samples in the same order as listed in the columns of the counts matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.

Example:

    ========== ============ =========
    **Sample** **Genotype** **Batch**

    Mut1       Mut          b1
    Mut2       Mut          b2
    Mut3       Mut          b3
    ========== ============ =========

*Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, edgeR will fit an additive linear model.

*Groups:* The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas.


**Gene Annotations:**
Optional input for gene annotations, this can contain more
information about the genes than just an ID number. The annotations will
be available in the differential expression results table and the optional normalised counts table.

Example:

    ==========  ==========  ===================================================
    **GeneID**  **Symbol**  **GeneName**
    ----------  ----------  ---------------------------------------------------
    1287        Pzp         pregnancy zone protein
    1298        Aanat       arylalkylamine N-acetyltransferase
    1302        Aatk        apoptosis-associated tyrosine kinase
    1303        Abca1       ATP-binding cassette, sub-family A (ABC1), member 1
    1304        Abca4       ATP-binding cassette, sub-family A (ABC1), member 4
    1305        Abca2       ATP-binding cassette, sub-family A (ABC1), member 2
    ==========  ==========  ===================================================

**Contrasts of Interest:**
The contrasts you wish to make between levels.
A common contrast would be a simple difference between two levels: "Mut-WT"
represents the difference between the mutant and wild type genotypes.
Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used.

**Filter Low Counts:**
Genes with very low counts across all libraries provide little evidence for differential expression.
In the biological point of view, a gene must be expressed at some minimal level before
it is likely to be translated into a protein or to be biologically important. In addition, the
pronounced discreteness of these counts interferes with some of the statistical approximations
that are used later in the pipeline. These genes should be filtered out prior to further
analysis.
As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples
for any of the conditions. Users can set their own definition of genes being expressed. Usually
a gene is required to have a count of 5-10 in a library to be considered expressed in that
library. Users should also filter with count-per-million (CPM) rather than filtering on the
counts directly, as the latter does not account for differences in library sizes between samples.

Option to ignore the genes that do not show significant levels of
expression, this filtering is dependent on two criteria: CPM/count and number of samples. You can specify to filter on CPM (Minimum CPM) or count (Minimum Count) values:

    * **Minimum CPM:** This is the minimum count per million that a gene must have in at
      least the number of samples specified under Minimum Samples.

    * **Minimum Count:** This is the minimum count that a gene must have. It can be combined with either Filter
      on Total Count or Minimum Samples.

    * **Filter on Total Count:** This can be used with the Minimum Count filter to keep genes
      with a minimum total read count.

    * **Minimum Samples:** This is the number of samples in which the Minimum CPM/Count
      requirement must be met in order for that gene to be kept.

If the Minimum Samples filter is applied, only genes that exhibit a CPM/count greater than the required amount in at least the number of samples specified will be used for analysis. Care should be taken to
ensure that the sample requirement is appropriate. In the case of an experiment
with two experimental groups each with two members, if there is a change from
insignificant CPM/count to significant CPM/count but the sample requirement is set to 3,
then this will cause that gene to fail the criteria. When in doubt simply do not
filter or consult the `limma User's Guide`_ for filtering recommendations.

**Advanced Options:**

By default error rate for multiple testing is controlled using Benjamini and
Hochberg's false discovery rate control at a threshold value of 0.05. However
there are options to change this to custom values.

    * **Minimum log2-fold-change Required:**
      In addition to meeting the requirement for the adjusted statistic for
      multiple testing, the observation must have an absolute log2-fold-change
      greater than this threshold to be considered significant, thus highlighted
      in the MD plot.

    * **Adjusted Threshold:**
      Set the threshold for the resulting value of the multiple testing control
      method. Only observations whose statistic falls below this value is
      considered significant, thus highlighted in the MD plot.

    * **P-Value Adjustment Method:**
      Change the multiple testing control method, the options are BH(1995) and
      BY(2001) which are both false discovery rate controls. There is also
      Holm(1979) which is a method for family-wise error rate control.

**Normalisation Method:**
The most obvious technical factor that affects the read counts, other than gene expression
levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression
analysis for varying sequencing depths as represented by differing library sizes. This is
part of the basic modeling procedure and flows automatically into fold-change or p-value
calculations. It is always present, and doesn’t require any user intervention.
The second most important technical influence on differential expression is one that is less
obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA
sample, but does not provide any measure of the total RNA output on a per-cell basis.
This commonly becomes important when a small number of genes are very highly expressed
in one sample, but not in another. The highly expressed genes can consume a substantial
proportion of the total library size, causing the remaining genes to be under-sampled in that
sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely
appear to be down-regulated in that sample . The edgeR `calcNormFactors` function normalizes for RNA composition by finding a set of scaling factors for the library sizes that minimize the log-fold changes between the samples for most genes. The default method for computing these scale factors uses a trimmed mean of M values (TMM) between each pair of samples. We call the product of the original library size and the scaling factor the *effective library size*. The effective library size replaces the original library size in all downsteam analyses. TMM is the recommended method for most RNA-Seq data where the majority (more than half) of the genes are believed not differentially expressed between any pair of the samples. You can change the normalisation method under **Advanced Options** above. For more information, see the `calcNormFactors` section in the `edgeR User's Guide`_.

**Robust Settings**
Option to use robust settings with eBayes, used by both liamm-voom and limma-trend. Using robust settings is usually recommended to protect against outlier genes, for more information see the `limma User's Guide`_. This is turned on by default.

**Prior Count:**
If the limma-trend method is used, a count (`prior.count`) is added to all counts to avoid taking a log of zero, and damp down the variances of logarithms of low counts. A default of 3 is used, as recommended in the `limma User's Guide`_.

**Apply Sample Weights:**
If the limma-voom method is used, an option is available to downweight outlier samples, such that their information is still
used in the statistical analysis but their impact is reduced. Use this
whenever significant outliers are present. The MDS plotting tool in this package
is useful for identifying outliers. For more information on this option see Liu et al. (2015).


**Outputs**

This tool outputs

    * a table of differentially expressed genes for each contrast of interest
    * a HTML report with plots and additional information

Optionally, under **Output Options** you can choose to output

    * a normalised counts table
    * an RData file

-----

**Citations:**

Please try to cite the appropriate articles when you publish results obtained using software, as such citation is the main means by which the authors receive credit for their work.

limma

Please cite the paper below for the limma software itself. Please also try
to cite the appropriate methodology articles that describe the statistical
methods implemented in limma, depending on which limma functions you are
using.  The methodology articles are listed in Section 2.1 of the `limma
User's Guide`_.

    * Smyth GK (2005). Limma: linear models for microarray data. In:
      'Bioinformatics and Computational Biology Solutions using R and
      Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry,
      W. Huber (eds), Springer, New York, pages 397-420.

    * Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic,
      A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights
      for microarray data. BMC Bioinformatics 7, Article 261.


edgeR

Please cite the first paper for the software itself and the other papers for
the various original statistical methods implemented in edgeR.  See
Section 1.2 in the `edgeR User's Guide`_ for more detail.

    * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor
      package for differential expression analysis of digital gene expression
      data. Bioinformatics 26, 139-140

      of multifactor RNA-Seq experiments with respect to biological variation.
      Nucleic Acids Research 40, 4288-4297

Please report problems or suggestions to: [e-mail]

.. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html
.. _limma approach: https://www.ncbi.nlm.nih.gov/pubmed/25605792
.. _limma User's Guide: http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf
.. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
.. _edgeR User's Guide: https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
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