hicexplorer_hicplottads: hicPlotTADs.xml comparison

comparison 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

comparison

equal deleted inserted replaced

-:94fff1a6a899
+:7e535e3b71f3
 <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>
 </macros>
 <expand macro="requirements" />
 #if $x_axis.where:
 where = $x_axis.where
 #end if
 #end if
 #for $counter, $track in enumerate($tracks):
 #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
 title = $track.track_file_style_conditional.title
 #if $track.track_file_style_conditional.depth:
 colormap = $track.track_file_style_conditional.colormap
 #end if
 #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:
 max_value = $track.track_file_style_conditional.max_value
 #end if
 transform = $track.track_file_style_conditional.transform
 width = $track.track_file_style_conditional.width_matrix
 #if $track.track_file_style_conditional.boundaries_file:
 #end if
 #if $track.track_file_style_conditional.scale_factor:
 scale factor = $track.track_file_style_conditional.scale_factor
 #end if
 #end if
 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
 [tad_score_$counter]
 file = $track.track_file_style_conditional.track_input_bedgraph
 title = $track.track_file_style_conditional.title
 file_type = bedgraph_matrix
 #else:
 file_type = bedgraph
 #end if
 type = lines
 #end if
 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
 [chrom states_$counter]
 file = $track.track_file_style_conditional.track_input_bed
 title = $track.track_file_style_conditional.title
 [genes_$counter]
 file = $track.track_file_style_conditional.track_input_bed
 title = $track.track_file_style_conditional.title
 #if $track.track_file_style_conditional.color:
 color = $track.track_file_style_conditional.color
 #end if
 #if $track.track_file_style_conditional.width_bed:
 width = $track.track_file_style_conditional.width_bed
 #end if
 #if $track.track_file_style_conditional.labels:
 labels = $track.track_file_style_conditional.labels
 #end if
 #if $track.track_file_style_conditional.type:
 type = $track.track_file_style_conditional.type
 #end if
 file_type = bed
 #if $track.track_file_style_conditional.fontsize:
 fontsize = $track.track_file_style_conditional.fontsize
 #end if
 #if $track.track_file_style_conditional.gene_rows:
 gene rows = $track.track_file_style_conditional.gene_rows
 #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
 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
 [bedgraph_$counter]
 file_type = bedgraph_matrix
 #else:
 file_type = bedgraph
 #end if
 type = lines
 #end if
 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
 [bigwig_$counter]
 file = $track.track_file_style_conditional.track_input_bigwig
 nans to zeros = $track.track_file_style_conditional.nans_to_zeros
 #if $track.track_file_style_conditional.type_conditional == 'fill_option':
 type = fill
 #elif $track.track_file_style_conditional.type_conditional == 'line_option':
 type = line:$track.track_file_style_conditional.type_conditional.width_line
 #elif $track.track_file_style_conditional.type_conditional == 'point_option':
 type = points:$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
 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
 [bedgraph_matrix_$counter]
 file = $track.track_file_style_conditional.track_input_bedgraph_matrix
 title = $track.track_file_style_conditional.title
 #if $track.track_file_style_conditional.type_lines:
 type = $track.track_file_style_conditional.type_lines
 #end if
 file_type = bedgraph_matrix
 plot horizontal lines=False
 #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
 #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 for</configfile>
 </configfiles>
 <inputs>
 <expand macro="region" />
 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph">
 <conditional name="track_file_style_conditional">
 <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="gene_track_option">Gene track / Bed track</option>
 <option value="bigwig_track_option">Bigwig track</option>
 <option value="bedgraph_track_option">Bedgraph track </option>
 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
 <option value="vlines_track_option">Vlines track</option>
 <option value="spacer_option">Spacer</option>
 </param>
 <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"/>
 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
 <param name="transform" type="select" label="Plot the transformed value">
 <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>
 </param>
 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false"
 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
 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" />
 </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"
 label="Plot labels" />
 </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"/>
 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
 label="Plot labels" />
 </param>
 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false"
 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" />
 </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"
 label="NAN's to zeros" />
 <conditional name="type_conditional">
 </when>
 <when value="fill_option" />
 </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"/>
 <param name="width_bedgraph" type="float" value="1.5" optional="True" label="Width"/>
 </when>
 <when value="spacer_option">
 <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>
 <option value="yes">Yes</option>
 </param>
 <option value="png">png</option>
 <option value="svg">svg</option>
 </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" />
 </change_format>
 </data>
 <tests>
 <test>
 <param name="region" value="chrX:3000000-3500000"/>
 <conditional name="x_axis">
 <param name="x_axis_select" value="yes" />
 </conditional>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="hic_matrix_option" />
 <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
 <param name="colormap" value="RdYlBu_r" />
 <param name="depth" value="200000" />
 <param name="transform" value="log1p" />
 <param name="boundaries_file" value="domains.bed" />
 <param name="x_labels" value="True" />
 </conditional>
 </repeat>
 <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" />
 </conditional>
 </repeat>
 <param name="track_file_style_selector" value="chrom_states_option" />
 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
 <param name="title" value="TAD state" />
 <param name="width_chrom" value="0.5" />
 <param name="labels" value="off" />
 </conditional>
 </repeat>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="tad_score_track_option" />
 <param name="track_input_bedgraph" value="tad_score.gz" ftype="bedgraph" />
 <param name="title" value="TAD separation score (Ramirez et al.)" />
 <param name="width_tad" value="10" />
 </conditional>
 </repeat>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="spacer_option" />
 <param name="spacer_width" value="1" />
 </conditional>
 </repeat>
 <param name="track_file_style_selector" value="bedgraph_track_option" />
 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
 <param name="title" value="bedgraph" />
 <param name="width_bedgraph" value="4" />
 <param name="color" value="blue" />
 </conditional>
 </repeat>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="bigwig_track_option" />
 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
 <param name="width_bigwig" value="4" />
 <param name="color" value="blue" />
 <conditional name="type_conditional">
 <param name="type_selector" value="fill_option" />
 </conditional>
 </conditional>
 </repeat>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="bigwig_track_option" />
 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
 <param name="title" value="rep 1 test line" />
 <param name="color" value="red" />
 <conditional name="type_conditional">
 <param name="type_selector" value="line_option" />
 <param name="width_line" value="1" />
 </conditional>
 </conditional>
 </repeat>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="bigwig_track_option" />
 <param name="width_bigwig" value="4" />
 <param name="color" value="red" />
 <conditional name="type_conditional">
 <param name="type_selector" value="line_option" />
 <param name="width_line" value="0.1" />
 </conditional>
 </conditional>
 </repeat>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="bigwig_track_option" />
 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
 <param name="title" value="rep 1 test point:0.5" />
 <param name="width_bigwig" value="4" />
 <param name="color" value="black" />
 <conditional name="type_conditional">
 <param name="type_selector" value="point_option" />
 <param name="width_point" value="0.5" />
 </conditional>
 </conditional>
 </repeat>
 <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" />
 </conditional>
 </repeat>
 <param name="track_file_style_selector" value="gene_track_option" />
 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
 <param name="title" value="genes" />
 <param name="width_bed" value="5" />
 <param name="fontsize" value="10" />
 </conditional>
 </repeat>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="spacer_option" />
 <param name="spacer_width" value="1" />
 </conditional>
 </repeat>
 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
 <param name="title" value="max num rows 3" />
 <param name="width_bed" value="3" />
 <param name="fontsize" value="8" />
 <param name="gene_rows" value="3" />
 </conditional>
 </repeat>
 <repeat name="tracks">
 <conditional name="track_file_style_conditional">
 <param name="track_file_style_selector" value="spacer_option" />
 <param name="spacer_width" value="1" />
 </conditional>
 </repeat>
 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
 <param name="title" value="bed6 global max row" />
 <param name="width_bed" value="20" />
 <param name="fontsize" value="10" />
 <param name="global_max_row" value="True" />
 </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>
 </repeat>
 <param name="image_file_format" value="png" />
 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
 </test>
 </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:
+This tool takes various types of tracks as input:
-- the contact matrix
-- Boundaries file: The result of ``hicFindTADs``.
+- **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.
-- different tracks for comparison:
+- **Chromatin states:** display blocks of different colors following a bed file.
-- Chromatine states:
+- **TAD score:** display TAD seperation score computed by ``hicFindTADs``.
-- TAD score
+- **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off.
-- gene tracks
+- **Bigwig track:** generic bigwig track plotting.
-- Generic bigwig, bedgraph or bedgraph matrix files
+- **Bedgraph track:** generic bedgraph track plotting.
-- Vlines: vertical lines as a visual support where regions start / end over all tracks
+- **Bedgraph matrix track** is used to specifically plot bm files computed by ``hicFindTADs`` (TAD seperation scores).
-- Spacer: Add some space between the different tracks
+- **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.
+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>

Mercurial > repos > bgruening > hicexplorer_hicplottads

comparison hicPlotTADs.xml @ 8:7e535e3b71f3 draft