Mercurial > repos > bgruening > hicexplorer_hicaggregatecontacts
diff hicAggregateContacts.xml @ 0:ccd1d3013827 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
| author | bgruening |
|---|---|
| date | Wed, 07 Mar 2018 03:37:18 -0500 |
| parents | |
| children | ec59bf4c3d06 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicAggregateContacts.xml Wed Mar 07 03:37:18 2018 -0500 @@ -0,0 +1,194 @@ +<tool id="hicexplorer_hicaggregatecontacts" name="@BINARY@" version="@WRAPPER_VERSION@.0"> + <description>Takes a list of positions in the hic-matrix and makes a pooled image</description> + <macros> + <token name="@BINARY@">hicAggregateContacts</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +@BINARY@ + --matrix '$matrix_h5_cooler' + --BED $BED + #if $BED2: + --BED2 $BED2 + #end if + + --range $range_min:$range_max + + --numberOfBins $numberOfBins + + --transform $transform + --avgType $avgType + + #if $outputs and 'PrefixMatrix' in $outputs: + --outFilePrefixMatrix 'matrix_values' + #end if + + #if $outputs and 'ClusterContactPositions' in $outputs: + --outFilePrefixClusterContactPositions 'contact_positions' + #end if + + #if $outputs and 'HeatmapFile' in $outputs: + --diagnosticHeatmapFile 'heatmap' + #end if + + #if $clustering: + $clustering + #end if + $clusterOnDiagonal + + #if $chromosomes: + --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])# + #end if + + #if $plotType: + --plotType $plotType + #end if + + #if $colormap: + --colorMap $colormap + #end if + + #if $vMin: + --vMin $vMin + #end if + + #if $vMax: + --vMax $vMax + #end if + + --outFileName plot.$image_file_format + && mv plot.$image_file_format plot + +]]> + </command> + <inputs> + <expand macro='matrix_h5_cooler_macro' /> + <param argument="--BED" type="data" format="bed" label="Interactions between regions in this BED file are plotted."/> + <param argument="--BED2" type="data" format="bed" optional="true" + label="Interactions between regions in first and second BED file are plotted."/> + + <expand macro='range' /> + + <repeat name="chromosomes" title="List of chromosomes to plot" min="0"> + <param name="chromosome" type="text"> + <validator type="empty_field" /> + </param> + </repeat> + + <param argument="--numberOfBins" type="integer" optional="true" label="Number of bins to include in the submatrix" + help=" The bed regions will be centered between - half number of bins + and the other half number of bins." /> + + <param argument="--transform" type="select" label="Type of transformation for the matrix" + help="If total counts are selected, then the sub-matrix values + are divided by the total counts for normalization. If + z-score or obs/exp are selected, then H-C matrix is + converted into a z-score or observed / expected matrix."> + <option value="none" selected="true">none</option> + <option value="total-counts">total-counts</option> + <option value="z-score">z-score</option> + <option value="obs/exp">obs/exp</option> + </param> + + <param argument="--avgType" type="select" label="Type of average to compute final matrix"> + <option value="median" selected="true">median</option> + <option value="mean">mean</option> + </param> + + <param name="clustering" type="select" optional="true" label="Number of clusters per chromosome" + help="When this option is set, then the matrix is split into + clusters using the hierarchical clustering algorithm, + using 'ward linkage'. --hclust could be very slow if + you have >1000 submatrices per chromosome. In those + cases, you might prefer --kmeans"> + <option value="--kmeans">kmenas</option> + <option value="--hclust">hclust (#clusters per chromosome)</option> + </param> + + <param argument="--clusterOnDiagonal" type="boolean" truevalue="--clusterOnDiagonal" falsevalue="" + label="Perform clustering on the submatrix diagonal" + help="Clustering is by default carried out on the whole + submatrices. If this parameter is given, the + clustering is only carried out based on the submatrix + diagonal (representing values at the same distance to each other)" /> + + <param argument="--plotType" type="select" optional="true" label="Plot type"> + <option value="2d">2D</option> + <option value="3d">3D</option> + </param> + <expand macro="colormap" /> + <param argument="--vMin" type="float" optional="true" label="vMin"/> + <param argument="--vMax" type="float" optional="true" label="vMax"/> + + <param name="image_file_format" type="select" label="Image output format"> + <option value="png" selected="True">png</option> + <option value="svg">svg</option> + </param> + + <param name="outputs" type="select" optional="true" multiple="true" label="Optional output files"> + <option value="PrefixMatrix">Save values underlying the final matrix</option> + <option value="ClusterContactPositions">Save the position of the contacts</option> + <option value="HeatmapFile">Heatmap file per chromosome</option> + </param> + + </inputs> + <outputs> + <data name="outFileName" from_work_dir="plot" format="png" label="${tool.name} on ${on_string}"> + <change_format> + <when input="image_file_format" value="svg" format="svg" /> + </change_format> + </data> + <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values"> + <discover_datasets pattern="matrix_values_(?P<designation>.*)\..*" directory="./" format="tabular" /> + </collection> + <collection name="contact_positions" type="list" label="${tool.name} on ${on_string}: Matrix values"> + <discover_datasets pattern="contact_positions_(?P<designation>.*)\..*" directory="./" format="tabular" /> + </collection> + <collection name="heatmap" type="list" label="${tool.name} on ${on_string}: Matrix values"> + <discover_datasets pattern="heatmap_(?P<designation>.*)\..*" directory="./" format="tabular" /> + </collection> + </outputs> + <tests> + <test> + <param name="matrix_h5_cooler" value="Li_et_al_2015.h5" ftype="h5"/> + <param name="BED" value="test_regions.bed" ftype="bed"/> + <param name="numberOfBins" value="30" /> + <param name="range_max" value="900000" /> + <param name="range_min" value="50000" /> + <param name="image_file_format" value="png" /> + <output name="outFileName" value="hicAggregateContacts_results1.png" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ + --outFilePrefixMatrix OUTFILEPREFIXMATRIX + If this option is given, then the values underlying + the final matrix will be saved to tab-delimited tables + (one per chromosome) using the indicated prefix, for + example TSS_to_TSS_chrX.tab. If clustering is + performed, then the values are saved including the + cluster_id a in TSS_to_TSS_chrX_cluster_1.tab + --outFilePrefixClusterContactPositions OUTFILEPREFIXCLUSTERCONTACTPOSITIONS + If this option is given, then the position of the + contacts is saved as (chrom1, start1, end1, chrom2, + start2, end2) where chrom_n, start_n, end_n correspond + to the pair ofpositions used to compute the submatrix. + The data is saved per chromosome and per cluster + separatedly (one file each) + --diagnosticHeatmapFile DIAGNOSTICHEATMAPFILE + If given, a heatmap file (per chromosome) is saved. + Each row in the heatmap contains thediagonal of each + of the submatrices centered on the bed file. This file + is useful to get an idea of the values that are used + for the aggregate matrix and to determine the fraction + of sub-matrices that are aggregated that may have an + enrichment at the center. + + + +| For more information about HiCExplorer please consider our documentation on readthedocs.io_ + +.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html +]]></help> + <expand macro="citations" /> +</tool>