Mercurial > repos > bgruening > deeptools_compute_matrix_operations
diff computeMatrixOperations.xml @ 0:1638c02b28b5 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
| author | bgruening |
|---|---|
| date | Mon, 05 Dec 2016 08:09:05 -0500 |
| parents | |
| children | 848ce8f81e6e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeMatrixOperations.xml Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,179 @@ +<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>