Mercurial > repos > bgruening > hicexplorer_hicplottads
diff hicPlotTADs.xml @ 8:7e535e3b71f3 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
| author | iuc |
|---|---|
| date | Fri, 27 Apr 2018 03:38:47 -0400 |
| parents | 94fff1a6a899 |
| children |
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--- a/hicPlotTADs.xml Wed Mar 07 03:46:02 2018 -0500 +++ b/hicPlotTADs.xml Fri Apr 27 03:38:47 2018 -0400 @@ -1,5 +1,5 @@ <tool id="hicexplorer_hicplottads" name="@BINARY@" version="@WRAPPER_VERSION@.0"> - <description>Plots the diagonal, and some values close to the diagonal of a HiC matrix</description> + <description>plot Hi-C contact matrices heatmaps alongside other data tracks</description> <macros> <token name="@BINARY@">hicPlotTADs</token> <import>macros.xml</import> @@ -30,7 +30,7 @@ #end if #end if #for $counter, $track in enumerate($tracks): -#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": +#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": [hic_section_$counter] file = $track.track_file_style_conditional.matrix_h5_cooler file_type = hic_matrix @@ -44,7 +44,7 @@ #if $track.track_file_style_conditional.min_value: min_value = $track.track_file_style_conditional.min_value #end if -#if $track.track_file_style_conditional.max_value: +#if $track.track_file_style_conditional.max_value: max_value = $track.track_file_style_conditional.max_value #end if transform = $track.track_file_style_conditional.transform @@ -65,7 +65,7 @@ scale factor = $track.track_file_style_conditional.scale_factor #end if -#end if +#end if #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option": [tad_score_$counter] @@ -91,7 +91,7 @@ file_type = bedgraph #end if type = lines -#end if +#end if #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option": [chrom states_$counter] @@ -116,34 +116,34 @@ title = $track.track_file_style_conditional.title #if $track.track_file_style_conditional.color: color = $track.track_file_style_conditional.color -#end if +#end if #if $track.track_file_style_conditional.width_bed: width = $track.track_file_style_conditional.width_bed -#end if +#end if #if $track.track_file_style_conditional.labels: labels = $track.track_file_style_conditional.labels -#end if +#end if #if $track.track_file_style_conditional.type: type = $track.track_file_style_conditional.type -#end if +#end if file_type = bed #if $track.track_file_style_conditional.fontsize: fontsize = $track.track_file_style_conditional.fontsize -#end if +#end if #if $track.track_file_style_conditional.gene_rows: gene rows = $track.track_file_style_conditional.gene_rows -#end if +#end if #if $track.track_file_style_conditional.global_max_row: global max row = $track.track_file_style_conditional.global_max_row -#end if +#end if -#end if +#end if #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option": @@ -168,7 +168,7 @@ file_type = bedgraph #end if type = lines -#end if +#end if #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option": @@ -195,14 +195,14 @@ type = fill #elif $track.track_file_style_conditional.type_conditional == 'line_option': type = line:$track.track_file_style_conditional.type_conditional.width_line -#elif $track.track_file_style_conditional.type_conditional == 'point_option': +#elif $track.track_file_style_conditional.type_conditional == 'point_option': type = points:$track.track_file_style_conditional.type_conditional.width_point #end if #if $track.track_file_style_conditional.data_range: show data range = $track.track_file_style_conditional.data_range #end if file_type = bigwig -#end if +#end if #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option": [bedgraph_matrix_$counter] @@ -223,21 +223,21 @@ #end if file_type = bedgraph_matrix plot horizontal lines=False -#end if +#end if #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": [vlines_$counter] file = $track.track_file_style_conditional.track_input_bed type = vlines file_type = bed -#end if +#end if #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": [spacer] #if $track.track_file_style_conditional.spacer_width: width = $track.track_file_style_conditional.spacer_width #end if -#end if +#end if #end for</configfile> </configfiles> <inputs> @@ -249,7 +249,7 @@ <param name="track_file_style_selector" type="select" label="Choose style of the track"> <option value="hic_matrix_option">TAD visualization</option> <option value="chrom_states_option">Chromatine states</option> - <option value="tad_score_track_option">TAD score</option> + <option value="tad_score_track_option">TAD score</option> <option value="gene_track_option">Gene track / Bed track</option> <option value="bigwig_track_option">Bigwig track</option> <option value="bedgraph_track_option">Bedgraph track </option> @@ -260,7 +260,7 @@ <when value="hic_matrix_option"> <expand macro="plot_title" /> <expand macro="matrix_h5_cooler_macro" /> - + <expand macro="colormap" /> <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> @@ -269,10 +269,10 @@ <option value="log1p" selected="True" >log1p</option> <option value="log">log</option> <option value="-log">-log</option> - + </param> <param name="width_matrix" type="float" value="1.5" optional="True" label="Width"/> - + <param name="type" type="select" optional="True" label="Plotting type"> <option value="arcplot">arcplot</option> <option value="interaction">interaction</option> @@ -292,14 +292,14 @@ label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead of the matrix set to lines if a heatmap representing the matrix is not wanted"/> <param name="width_tad" type="float" value="0.2" optional="True" label="Width"/> - <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> + <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> </when> <when value="chrom_states_option"> <expand macro="plot_title" /> - + <expand macro="track_input_bed_macro" /> <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> - + <param name="border_color" type="color" value="#000000" label="Border color" optional="True" /> <param name="width_chrom" type="float" value="1.5" optional="True" label="Width"/> <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" @@ -307,7 +307,7 @@ </when> <when value="gene_track_option"> <expand macro="plot_title" /> - + <expand macro="track_input_bed_macro" /> <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> <param name="width_bed" type="float" value="1.5" optional="True" label="Width"/> @@ -321,25 +321,25 @@ label="Global max rows" /> <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" /> <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> - + </when> <when value="bedgraph_track_option"> <expand macro="plot_title" /> <expand macro="track_input_bedgraph_macro" /> <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> - + <param name="width_bedgraph" type="float" value="0.2" optional="True" label="Width"/> - <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> + <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> </when> <when value="bigwig_track_option"> <expand macro="plot_title" /> - + <expand macro="track_input_bigwig_macro" /> <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> - + <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> <param name="max_value" type="float" value="" optional="True" label="Maximum value"/> - + <param name="width_bigwig" type="float" value="1.5" optional="True" label="Width"/> <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false" @@ -360,11 +360,11 @@ </conditional> <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" /> </when> - - + + <when value="bedgraph_matrix_track_option"> <expand macro="plot_title" /> - + <expand macro="track_input_bedgraph_matrix_macro" /> <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> <param name="max_value" type="float" value="" optional="True" label="Maximum value"/> @@ -382,10 +382,10 @@ <expand macro="spacer_macro" /> </when> </conditional> - + </repeat> - + <conditional name="x_axis"> <param name="x_axis_select" type="select" label="Configure x-axis"> <option value="no" selected="True">No</option> @@ -406,7 +406,7 @@ </param> </inputs> <outputs> - <data format="png" name="outFileName" from_work_dir="plot"> + <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on [${on_string}]: Plot"> <change_format> <when input="image_file_format" value="png" format="png" /> <when input="image_file_format" value="svg" format="svg" /> @@ -418,7 +418,7 @@ <param name="region" value="chrX:3000000-3500000"/> <conditional name="x_axis"> <param name="x_axis_select" value="yes" /> - </conditional> + </conditional> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hic_matrix_option" /> @@ -430,9 +430,9 @@ <param name="transform" value="log1p" /> <param name="boundaries_file" value="domains.bed" /> <param name="x_labels" value="True" /> - </conditional> + </conditional> </repeat> - <repeat name="tracks"> + <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_width" value="0.05" /> @@ -445,7 +445,7 @@ <param name="title" value="TAD state" /> <param name="width_chrom" value="0.5" /> <param name="labels" value="off" /> - </conditional> + </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> @@ -455,7 +455,7 @@ <param name="width_tad" value="10" /> </conditional> </repeat> - <repeat name="tracks"> + <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_width" value="1" /> @@ -468,7 +468,7 @@ <param name="title" value="bedgraph" /> <param name="width_bedgraph" value="4" /> <param name="color" value="blue" /> - </conditional> + </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> @@ -480,9 +480,9 @@ <conditional name="type_conditional"> <param name="type_selector" value="fill_option" /> </conditional> - </conditional> + </conditional> </repeat> - + <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> @@ -494,7 +494,7 @@ <param name="type_selector" value="line_option" /> <param name="width_line" value="1" /> </conditional> - </conditional> + </conditional> </repeat> <repeat name="tracks"> @@ -507,11 +507,11 @@ <conditional name="type_conditional"> <param name="type_selector" value="line_option" /> <param name="width_line" value="0.1" /> - + </conditional> - </conditional> + </conditional> </repeat> - + <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> @@ -522,12 +522,12 @@ <conditional name="type_conditional"> <param name="type_selector" value="point_option" /> <param name="width_point" value="0.5" /> - + </conditional> - </conditional> + </conditional> </repeat> - <repeat name="tracks"> + <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_width" value="0.5" /> @@ -540,9 +540,9 @@ <param name="title" value="genes" /> <param name="width_bed" value="5" /> <param name="fontsize" value="10" /> - </conditional> + </conditional> </repeat> - <repeat name="tracks"> + <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_width" value="1" /> @@ -556,9 +556,9 @@ <param name="width_bed" value="3" /> <param name="fontsize" value="8" /> <param name="gene_rows" value="3" /> - </conditional> + </conditional> </repeat> - <repeat name="tracks"> + <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_width" value="1" /> @@ -572,14 +572,14 @@ <param name="width_bed" value="20" /> <param name="fontsize" value="10" /> <param name="global_max_row" value="True" /> - </conditional> + </conditional> </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="vlines_track_option" /> <param name="track_input_bed" value="domains.bed" ftype="bed" /> <param name="type" value="vlines" /> - </conditional> + </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> @@ -587,38 +587,47 @@ </tests> <help><![CDATA[ -Plot TADs -========= +Plot Topologic Associated Domains +================================= -``hicPlotTADs`` is a visualization tool to plot the topologically associating domains (TADs) in a given region. Additional tracks can be added to enable the comparisons with other data like gene tracks. +**hicPlotTADs** is a visualization tool to plot the topologically associating domains (TADs) in a given region. Additional tracks can be added to enable the comparisons with other data like gene, ChIP-seq, RNA-seq or other tracks, including TAD seperation scores computed by ``hicFindTADs``. -Input +_________________ + +Usage ----- -- the region to plot: chr1:1000-2000 -- the tracks: - - the contact matrix - - Boundaries file: The result of ``hicFindTADs``. -- different tracks for comparison: - - Chromatine states: - - TAD score - - gene tracks - - Generic bigwig, bedgraph or bedgraph matrix files - - Vlines: vertical lines as a visual support where regions start / end over all tracks - - Spacer: Add some space between the different tracks + +This tool takes various types of tracks as input: -For each track parameters for the color, the width or the font size can be defined. + - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap. + - **Chromatin states:** display blocks of different colors following a bed file. + - **TAD score:** display TAD seperation score computed by ``hicFindTADs``. + - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off. + - **Bigwig track:** generic bigwig track plotting. + - **Bedgraph track:** generic bedgraph track plotting. + - **Bedgraph matrix track** is used to specifically plot bm files computed by ``hicFindTADs`` (TAD seperation scores). + - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by ``hicFindTADs``. + - **Spacer:** Add some space between two tracks. + +For each track, parameters for the color, the width or the font size can be defined. + +_________________ Output ------ -An output looks like this: +**hicPlotTADs** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) also contains Hi-C data. The plot is composed of tracks that need to be specified. +Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **hicPlotTADs**. TADs were computed by ``hicFindTADs``. The additional tracks added correspond to: TAD-separation score (as reported by ``hicFindTADs``), chromatin states, principal component 1 (A/B compartment) computed using ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_. -.. image:: $PATH_TO_IMAGES/master_TADs_plot.png - :width: 80 % +.. image:: $PATH_TO_IMAGES/hicPlotTADs.png + :width: 70 % + +_________________ | For more information about HiCExplorer please consider our documentation on readthedocs.io_ .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html +.. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9 ]]></help> <expand macro="citations" /> </tool>