<tool id="deeptools_compute_matrix_operations" name="computeMatrixOperations" version="@WRAPPER_VERSION@.0">
    <description>Modify or combine the output of computeMatrix in a variety of ways.</description>
    <macros>
        <token name="@BINARY@">computeMatrixOperations</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command>
<![CDATA[
        @BINARY@
            #if $submodule.command == "info":
                info
                -m $submodule.matrixFile
                > $outFileTxt
            #else if $submodule.command == "subset":
                subset
                -m $submodule.matrixFile
                #if $submodule.groups is not None and str($submodule.groups) != '':
                    --groups $submodule.groups
                #end if
                #if $submodule.samples is not None and str($submodule.samples) != '':
                    --samples $submodule.samples
                #end if
                -o $outFileName
            #else if $submodule.command == "filterStrand":
                filterStrand
                -m $submodule.matrixFile
                --strand $submodule.strand
                -o $outFileName
            #else if $submodule.command == "rbind":
                #set $files=[]
                #for $f in $submodule.matrixFiles:
                    #silent $files.append(str($f.matrixFile))
                #end for
                rbind
                -m '#echo "' '".join($files)#'
                -o $outFileName
            #else if $submodule.command == "cbind":
                cbind
                #set $files=[]
                #for $f in $submodule.matrixFiles:
                    #silent $files.append(str($f.matrixFile))
                #end for
                -m '#echo "' '".join($files)#'
                -o $outFileName
            #else if $submodule.command == "sort":
                sort
                #set $files=[]
                #for $f in $submodule.regionsFiles:
                    #silent $files.append(str($f.regionsFile))
                #end for
                -m $submodule.matrixFile
                -R '#echo "' '".join($files)#'
                -o $outFileName
            #end if
]]>
    </command>
    <inputs>
        <conditional name="submodule">
            <param name="command" type="select" label="Operation type">
                <option value="info" selected="true">Print information (info)</option>
                <option value="subset">Subset by samples and/or groups of regions (subset)</option>
                <option value="filterStrand">Filter by strand (filterStrand)</option>
                <option value="rbind">Bind matrices, top to bottom (rbind)</option>
                <option value="cbind">Bind matrices, left to right (cbind)</option>
                <option value="sort">Sort by region order in specified files (sort)</option>
            </param>
            <when value="info">
                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
                       label="Matrix file from the computeMatrix tool" help=""/>
            </when>

            <when value="subset">
                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
                       label="Matrix file from the computeMatrix tool" help=""/>
                <param argument="groups" type="text" optional="true" label="Region groups to include."
                    help="If blank, all region groups are output. Alternatively, one or more groups listed in the output of the 'info' command can be used (separate groups by a space and enclose in quotes if needed)" />
                <param argument="samples" type="text" optional="true" label="Samples to include."
                    help="If blank, all samples are output. Alternatively, one or more samples listed in the output of the 'info' command can be used (separate sample names by a space and enclose in quotes if needed)" />
            </when>

            <when value="filterStrand">
                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
                       label="Matrix file from the computeMatrix tool" help=""/>
                <param argument="strand" type="select" label="Only include regions on this strand."
                    help="Only regions on the desired strand will be included in the output. If you desire to instead remove regions on only one strand (or the . strand), separately run this on the other strand and then use the rbind operation.">
                    <option value="+">+</option>
                    <option value="-">-</option>
                    <option value=".">. (no annotated strand)</option>
                </param>
            </when>

            <when value="rbind">
                <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
                       label="Matrix file from the computeMatrix tool" help=""/>
                </repeat>
            </when>

            <when value="cbind">
                <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
                       label="Matrix file from the computeMatrix tool" help=""/>
                </repeat>
            </when>

            <when value="sort">
                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
                       label="Matrix file from the computeMatrix tool" help=""/>
                <repeat name="regionsFiles" title="BED or GTF files of regions" min="1">
                    <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot"
                        help="File, in BED format, containing the regions to plot."/>
                </repeat>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} ${submodule.command} on ${on_string}">
            <filter>
            ((
                submodule['command'] != "info"
            ))
            </filter>
        </data>
        <data format="txt" name="outFileTxt" label="${tool.name} info on ${on_string}">
            <filter>
            ((
                submodule['command'] == "info"
            ))
            </filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="command" value="info" />
            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
            <output name="outFileTxt" file="computeMatrixOperations.txt" ftype="txt" />
        </test>
        <test>
            <param name="command" value="rbind" />
            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
            <output name="outFileName" file="computeMatrixOperations_result2.mat.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" delta="100"/>
        </test>
    </tests>
    <help>
<![CDATA[

What it does
------------

``computeMatrixOperations`` can perform a variety of operations on one or more files produced by ``computeMatrix`` (N.B., the output is always written to a new file):

+----------------+--------------------------------------------------------------------------------------------------------------------------+
+ **Subcommand** | **What it does**                                                                                                         |
+----------------+--------------------------------------------------------------------------------------------------------------------------+
+ info           | Prints out the sample and region group names in the order in which they appear.                                          |
+----------------+--------------------------------------------------------------------------------------------------------------------------+
+ subset         | Subsets a file by the desired samples/region group names. This can also change the order of these samples/region groups. |
+----------------+--------------------------------------------------------------------------------------------------------------------------+
+ filterStrand   | Filters the file to only include regions annotated as being on a particular strand.                                      |
+----------------+--------------------------------------------------------------------------------------------------------------------------+
+ rbind          | Concatenates multiple matrices together, top to bottom.                                                                  |
+----------------+--------------------------------------------------------------------------------------------------------------------------+
+ cbind          | Merges multiple matrices, left to right.                                                                                 |
+----------------+--------------------------------------------------------------------------------------------------------------------------+
+ sort           | Sorts the given file so regions are in the order of occurence in the input BED/GTF file(s).                              |
+----------------+--------------------------------------------------------------------------------------------------------------------------+


These operations are useful when you want to run computeMatrix on multiple files (thereby keeping all of the values together) and later exclude regions/samples or add new ones. Another common use would be if you require the output of computeMatrix to be sorted to match the order of regions in the input file.

-----

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>