Mercurial > repos > iuc > pygenometracks
changeset 2:c171f2b7d76e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
| author | iuc |
|---|---|
| date | Fri, 23 Aug 2019 07:24:20 -0400 |
| parents | 0ea86f6bf2a1 |
| children | feab9265552d |
| files | macros.xml pyGenomeTracks.xml test-data/bigwig_multiple.png test-data/bigwig_multiple_before.png test-data/dm3_genes.bed6.gz test-data/dm3_subset_BDGP5.78.gtf.gz test-data/dm3_subset_BDGP5.78_asbed4.bed.gz test-data/master_TADs_BW_plot.png test-data/master_TADs_plot.png test-data/master_TADs_plot_before.png test-data/test_alpha.png test-data/test_gtf_bed4.png test-data/test_with_neg_values.bg.gz |
| diffstat | 13 files changed, 645 insertions(+), 127 deletions(-) [+] |
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--- a/macros.xml Mon Jul 02 19:32:13 2018 -0400 +++ b/macros.xml Fri Aug 23 07:24:20 2019 -0400 @@ -1,12 +1,13 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">2.0</token> + <token name="@WRAPPER_VERSION@">3.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement> + <!--<requirement type="package" version="3.7">python</requirement>--> <yield /> </requirements> - <version_command>@BINARY@ --version</version_command> + <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command> </xml> <xml name="citations"> @@ -188,6 +189,9 @@ <xml name="track_input_bed_macro"> <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple='True'/> </xml> + <xml name="track_input_bed_gtf_macro"> + <param name="track_input_bed" type="data" format="bed,gtf" label="Track file bed or gtf format" multiple='True'/> + </xml> <xml name="track_input_bed_single_macro"> <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/> </xml> @@ -207,4 +211,219 @@ <param name="spacer_height" type="float" value="" optional="True" label="Include spacer at the end of the track" help="Height of the spacer." /> </xml> + <xml name="inverted_macro"> + <param name="invert_orientation" type="boolean" truevalue="yes" falsevalue="no" checked="false" + label="Invert the track" /> + </xml> + <xml name="color_bed_macro"> + <conditional name="color_bed"> + <param name="color_bed_select" type="select" label="Use color:"> + <option value="manually" selected="True">manually</option> + <option value="bed_rgb">From the 9th field</option> + <option value="colormap">From the 5th field (score)</option> + </param> + <when value="manually"> + <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> + </when> + <when value="bed_rgb" /> + <when value="colormap"> + <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> + <option value="RdYlBu">RdYlBu</option> + <option value="Accent">Accent</option> + <option value="Spectral">Spectral</option> + <option value="Set1">Set1</option> + <option value="Set2">Set2</option> + <option value="Set3">Set3</option> + <option value="Dark2">Dark2</option> + <option value="Reds">Reds</option> + <option value="Oranges">Oranges</option> + <option value="Greens">Greens</option> + <option value="Blues">Blues</option> + <option value="Greys">Greys</option> + <option value="Purples">Purples</option> + <option value="Paired">Paired</option> + <option value="Pastel1">Pastel1</option> + <option value="Pastel2">Pastel2</option> + <option value="spring">spring</option> + <option value="summer">summer</option> + <option value="autumn">autumn</option> + <option value="winter">winter</option> + <option value="hot">hot</option> + <option value="coolwarm">coolwarm</option> + <option value="cool">cool</option> + <option value="seismic">seismic</option> + <option value="terrain">terrain</option> + <option value="ocean">ocean</option> + <option value="rainbow">rainbow</option> + <option value="bone">bone</option> + <option value="flag">flag</option> + <option value="prism">prism</option> + <option value="cubehelix">cubehelix</option> + <option value="binary">binary</option> + <option value="pink">pink</option> + <option value="gray">gray</option> + <option value="copper">copper</option> + <option value="BrBG">BrBG</option> + <option value="BuGn">BuGn</option> + <option value="BuPu">BuPu</option> + <option value="GnBu">GnBu</option> + <option value="OrRd">OrRd</option> + <option value="PiYG">PiYG</option> + <option value="PRGn">PRGn</option> + <option value="PuOr">PuOr</option> + <option value="PuRd">PuRd</option> + <option value="PuBu">PuBu</option> + <option value="RdBu">RdBu</option> + <option value="RdGy">RdGy</option> + <option value="RdPu">RdPu</option> + <option value="YlGn">YlGn</option> + <option value="PuBuGn">PuBuGn</option> + <option value="RdYlGn">RdYlGn</option> + <option value="YlGnBu">YlGnBu</option> + <option value="YlOrBr">YlOrBr</option> + <option value="YlOrRd">YlOrRd</option> + <option value="gist_gray">gist_gray</option> + <option value="gist_stern">gist_stern</option> + <option value="gist_earth">gist_earth</option> + <option value="gist_yarg">gist_yarg</option> + <option value="gist_ncar">gist_ncar</option> + <option value="gist_rainbow">gist_rainbow</option> + <option value="gist_heat">gist_heat</option> + <option value="gnuplot">gnuplot</option> + <option value="gnuplot2">gnuplot2</option> + <option value="CMRmap">CMRmap</option> + <option value="bwr">bwr</option> + <option value="hsv">hsv</option> + <option value="brg">brg</option> + <option value="jet">jet</option> + <option value="afmhot">afmhot</option> + <option value="Accent_r">Accent reversed</option> + <option value="Spectral_r">Spectral reversed</option> + <option value="Set1_r">Set1 reversed</option> + <option value="Set2_r">Set2 reversed</option> + <option value="Set3_r">Set3 reversed</option> + <option value="Dark2_r">Dark2 reversed</option> + <option value="Reds_r">Reds reversed</option> + <option value="Oranges_r">Oranges reversed</option> + <option value="Greens_r">Greens reversed</option> + <option value="Blues_r">Blues reversed</option> + <option value="Greys_r">Greys reversed</option> + <option value="Purples_r">Purples reversed</option> + <option value="Paired_r">Paired reversed</option> + <option value="Pastel1_r">Pastel1 reversed</option> + <option value="Pastel2_r">Pastel2 reversed</option> + <option value="spring_r">spring reversed</option> + <option value="summer_r">summer reversed</option> + <option value="autumn_r">autumn reversed</option> + <option value="winter_r">winter reversed</option> + <option value="hot_r">hot reversed</option> + <option value="coolwarm_r">coolwarm reversed</option> + <option value="cool_r">cool reversed</option> + <option value="seismic_r">seismic reversed</option> + <option value="terrain_r">terrain reversed</option> + <option value="ocean_r">ocean reversed</option> + <option value="rainbow_r">rainbow reversed</option> + <option value="bone_r">bone reversed</option> + <option value="flag_r">flag reversed</option> + <option value="prism_r">prism reversed</option> + <option value="cubehelix_r">cubehelix reversed</option> + <option value="binary_r">binary reversed</option> + <option value="pink_r">pink reversed</option> + <option value="gray_r">gray reversed</option> + <option value="copper_r">copper reversed</option> + <option value="BrBG_r">BrBG reversed</option> + <option value="BuGn_r">BuGn reversed</option> + <option value="BuPu_r">BuPu reversed</option> + <option value="GnBu_r">GnBu reversed</option> + <option value="OrRd_r">OrRd reversed</option> + <option value="PiYG_r">PiYG reversed</option> + <option value="PRGn_r">PRGn reversed</option> + <option value="PuOr_r">PuOr reversed</option> + <option value="PuRd_r">PuRd reversed</option> + <option value="PuBu_r">PuBu reversed</option> + <option value="RdBu_r">RdBu reversed</option> + <option value="RdGy_r">RdGy reversed</option> + <option value="RdPu_r">RdPu reversed</option> + <option value="YlGn_r">YlGn reversed</option> + <option value="PuBuGn_r">PuBuGn reversed</option> + <option value="RdYlBu_r" selected="True">RdYlBu reversed</option> + <option value="RdYlGn_r">RdYlGn reversed</option> + <option value="YlGnBu_r">YlGnBu reversed</option> + <option value="YlOrBr_r">YlOrBr reversed</option> + <option value="YlOrRd_r">YlOrRd reversed</option> + <option value="gist_gray_r">gist_gray reversed</option> + <option value="gist_stern_r">gist_stern reversed</option> + <option value="gist_earth_r">gist_earth reversed</option> + <option value="gist_yarg_r">gist_yarg reversed</option> + <option value="gist_ncar_r">gist_ncar reversed</option> + <option value="gist_rainbow_r">gist_rainbow reversed</option> + <option value="gist_heat_r">gist_heat reversed</option> + <option value="gnuplot_r">gnuplot reversed</option> + <option value="gnuplot2_r">gnuplot2 reversed</option> + <option value="CMRmap_r">CMRmap reversed</option> + <option value="bwr_r">bwr reversed</option> + <option value="hsv_r">hsv reversed</option> + <option value="brg_r">brg reversed</option> + <option value="jet_r">jet reversed</option> + <option value="afmhot_r">afmhot reversed</option> + </param> + </when> + </conditional> + <param name="border_color" type="color" value="#000000" label="Border color" optional="True" /> + </xml> + <xml name="color_coverage_macro"> + <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> + <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/> + <conditional name="color_negative"> + <param name="color_negative_select" type="select" label="Use a different color for negative values"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="color" type="color" value="#000000" label="Color of negative values" optional="True" /> + </when> + </conditional> + </xml> + <xml name="overlay_macro"> + <param name="overlay_select" type="select" label="Overlay this track with the previous one:"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + <option value="share-y">Yes and keep same y axis</option> + </param> + </xml> + <xml name="type_coverage_macro"> + <conditional name="type_conditional"> + <param name="type_selector" type="select" label="Choose style of the plot."> + <option value="fill_option">fill</option> + <option value="line_option">line</option> + <option value="point_option">point</option> + </param> + <when value="line_option"> + <param name="width_line" type="float" value="0.5" optional="True" label="Width"/> + </when> + <when value="point_option"> + <param name="width_point" type="float" value="0.5" optional="True" label="Width"/> + </when> + <when value="fill_option" /> + </conditional> + </xml> + <xml name="minmax_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"/> + </xml> + <xml name="reading_bw_macro"> + <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False"> + <param name="summary" type="select" label="Summary method"> + <option value="mean" selected="True">mean=mean value</option> + <option value="min">min=minimum value</option> + <option value="max">max=maximum value</option> + <option value="coverage">coverage=number of covered bases</option> + <option value="std">std=standard deviation</option> + </param> + <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" /> + </section> + </xml> </macros>
--- a/pyGenomeTracks.xml Mon Jul 02 19:32:13 2018 -0400 +++ b/pyGenomeTracks.xml Fri Aug 23 07:24:20 2019 -0400 @@ -7,6 +7,21 @@ <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ + #for $counter, $track in enumerate($tracks): + #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": + #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): + #set ext = $data_matrix.extension + ln -s $data_matrix ${counter}_${counter_matrix}.$ext && + #end for + #end if + #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": + #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): + #set ext = $data_bed.extension + ln -s $data_bed ${counter}_${counter_bed}.$ext && + #end for + #end if + #end for + sed '/^$/d' '$tracks_config' && @BINARY@ @@ -35,8 +50,9 @@ #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): -[hic_section_$counter] -file = $data_matrix +[hic_section_${counter}_${counter_matrix}] +#set ext = $data_matrix.extension +file = ${counter}_${counter_matrix}.$ext file_type = hic_matrix #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title @@ -55,29 +71,40 @@ #if $track.track_file_style_conditional.max_value: max_value = $track.track_file_style_conditional.max_value #end if +#if $track.track_file_style_conditional.transform != "": transform = $track.track_file_style_conditional.transform +#end if +#if $track.track_file_style_conditional.height_matrix != "": height = $track.track_file_style_conditional.height_matrix - -#if $track.track_file_style_conditional.boundaries_file is not None: -#set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix] -boundaries_file = $boundary_file #end if -#if $track.track_file_style_conditional.x_labels: -x labels = $track.track_file_style_conditional.x_labels -#end if -#if $track.track_file_style_conditional.type: -type = $track.track_file_style_conditional.type -#end if #if $track.track_file_style_conditional.show_masked_bins: show_masked_bins = $track.track_file_style_conditional.show_masked_bins #end if +#if $track.track_file_style_conditional.invert_orientation: +orientation = inverted +#end if #if $track.track_file_style_conditional.scale_factor: scale factor = $track.track_file_style_conditional.scale_factor #end if +#if str($track.track_file_style_conditional.boundaries_file) != "None": +#if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix: +#set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix] +#else: +#set boundary_file = $track.track_file_style_conditional.boundaries_file[0] +#end if +[tads_${counter}_${counter_matrix}] +file = $boundary_file +file_type = domains +border color = black +color = none +overlay previous = share-y +#end if + + +#if $track.track_file_style_conditional.spacer_height != "": [spacer] -#if $track.track_file_style_conditional.spacer_height: height = $track.track_file_style_conditional.spacer_height #end if #end for @@ -90,7 +117,7 @@ #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: [tad_score_$counter] -file = $data_bedgraph +file = $data_bedgraph #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #else: @@ -102,22 +129,21 @@ #if $track.track_file_style_conditional.height_tad: height = $track.track_file_style_conditional.height_tad #end if -#if $track.track_file_style_conditional.type_lines: -type = $track.track_file_style_conditional.type_lines -#end if #if $track.track_file_style_conditional.show_data: show data range = $track.track_file_style_conditional.show_data #end if #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) -#if $columns > 5: +#if $columns > 4: file_type = bedgraph_matrix +#if $track.track_file_style_conditional.type_lines: +type = $track.track_file_style_conditional.type_lines +#end if #else: file_type = bedgraph #end if -type = lines +#if $track.track_file_style_conditional.spacer_height != "": [spacer] -#if $track.track_file_style_conditional.spacer_height: height = $track.track_file_style_conditional.spacer_height #end if #end for @@ -136,19 +162,21 @@ #else: title = $data_bed.name #end if -#if $track.track_file_style_conditional.color: -color = $track.track_file_style_conditional.color +#if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": +color = bed_rgb +#elif $track.track_file_style_conditional.color_bed.color: +color = $track.track_file_style_conditional.color_bed.color +#end if +#if $track.track_file_style_conditional.border_color: +border color = $track.track_file_style_conditional.border_color #end if display = collapsed #if $track.track_file_style_conditional.height_chrom: height = $track.track_file_style_conditional.height_chrom #end if -#if $track.track_file_style_conditional.border_color: -border_color = $track.track_file_style_conditional.border_color -#end if file_type = bed +#if $track.track_file_style_conditional.spacer_height != "": [spacer] -#if $track.track_file_style_conditional.spacer_height: height = $track.track_file_style_conditional.spacer_height #end if #end for @@ -159,19 +187,33 @@ #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": -#for $data_bed in $track.track_file_style_conditional.track_input_bed: +#for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): -[genes_$counter] -file = $data_bed +[genes_${counter}_${counter_bed}] +#set ext = $data_bed.extension +file = ${counter}_${counter_bed}.$ext #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title #else: title = $data_bed.name #end if -#if $track.track_file_style_conditional.color: -color = $track.track_file_style_conditional.color +#if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": +color = bed_rgb +#elif $track.track_file_style_conditional.color_bed.color: +color = $track.track_file_style_conditional.color_bed.color +#end if +#if $track.track_file_style_conditional.border_color: +border color = $track.track_file_style_conditional.border_color #end if +#if $track.track_file_style_conditional.flybase: +style = flybase +#else +style = UCSC +#end if + +display = $track.track_file_style_conditional.display + #if $track.track_file_style_conditional.height_bed: height = $track.track_file_style_conditional.height_bed #end if @@ -180,10 +222,6 @@ 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 @@ -196,8 +234,8 @@ #if $track.track_file_style_conditional.global_max_row: global max row = $track.track_file_style_conditional.global_max_row #end if +#if $track.track_file_style_conditional.spacer_height != "": [spacer] -#if $track.track_file_style_conditional.spacer_height: height = $track.track_file_style_conditional.spacer_height #end if #end for @@ -211,28 +249,54 @@ file = $data_bedgraph #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title -#else: +#elif $track.track_file_style_conditional.overlay_select == "no": title = $data_bedgraph.name #end if #if $track.track_file_style_conditional.color: color = $track.track_file_style_conditional.color #end if +alpha = $track.track_file_style_conditional.alpha +#if $track.track_file_style_conditional.color_negative.color_negative_select == "yes": +negative color = $track.track_file_style_conditional.color_negative.color +#end if #if $track.track_file_style_conditional.height_bedgraph: height = $track.track_file_style_conditional.height_bedgraph #end if +#if $track.track_file_style_conditional.min_value: +min_value = $track.track_file_style_conditional.min_value +#else: +min_value = auto +#end if +#if $track.track_file_style_conditional.max_value: +max_value = $track.track_file_style_conditional.max_value +#else: +max_value = auto +#end if + #if $track.track_file_style_conditional.show_data: show data range = $track.track_file_style_conditional.show_data #end if #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) -#if $columns > 5: +#if $columns > 4: file_type = bedgraph_matrix +type = lines #else: file_type = bedgraph +#if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': +type = fill +#elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': +type = line:$track.track_file_style_conditional.type_conditional.width_line +#elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': +type = points:$track.track_file_style_conditional.type_conditional.width_point #end if -type = lines +#end if +#if $track.track_file_style_conditional.invert_orientation: +orientation = inverted +#end if +overlay previous = $track.track_file_style_conditional.overlay_select +#if $track.track_file_style_conditional.spacer_height != "": [spacer] -#if $track.track_file_style_conditional.spacer_height: height = $track.track_file_style_conditional.spacer_height #end if #end for @@ -244,10 +308,16 @@ file = $data_bigwig #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title -#else: +#elif $track.track_file_style_conditional.overlay_select == "no": title = $data_bigwig.name #end if +#if $track.track_file_style_conditional.color: color = $track.track_file_style_conditional.color +#end if +alpha = $track.track_file_style_conditional.alpha +#if $track.track_file_style_conditional.color_negative.color_negative_select == "yes": +negative color = $track.track_file_style_conditional.color_negative.color +#end if #if $track.track_file_style_conditional.min_value: min_value = $track.track_file_style_conditional.min_value #else: @@ -259,23 +329,28 @@ max_value = auto #end if height = $track.track_file_style_conditional.height_bigwig -#if $track.track_file_style_conditional.number_of_bins: -number of bins = $track.track_file_style_conditional.number_of_bins +summary method = $track.track_file_style_conditional.reading_bw_conditional.summary +nans to zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros +#if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins: +number of bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins #end if -nans to zeros = $track.track_file_style_conditional.nans_to_zeros -#if $track.track_file_style_conditional.type_conditional == 'fill_option': +#if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': type = fill -#elif $track.track_file_style_conditional.type_conditional == 'line_option': -type = line:$track.track_file_style_conditional.type_conditional.height_line -#elif $track.track_file_style_conditional.type_conditional == 'point_option': +#elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': +type = line:$track.track_file_style_conditional.type_conditional.width_line +#elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': type = points:$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 +#if $track.track_file_style_conditional.invert_orientation: +orientation = inverted +#end if +overlay previous = $track.track_file_style_conditional.overlay_select +#if $track.track_file_style_conditional.spacer_height != "": [spacer] -#if $track.track_file_style_conditional.spacer_height: height = $track.track_file_style_conditional.spacer_height #end if #end for @@ -307,8 +382,11 @@ #end if file_type = bedgraph_matrix plot horizontal lines=False +#if $track.track_file_style_conditional.invert_orientation: +orientation = inverted +#end if +#if $track.track_file_style_conditional.spacer_height != "": [spacer] -#if $track.track_file_style_conditional.spacer_height: height = $track.track_file_style_conditional.spacer_height #end if #end for @@ -323,8 +401,8 @@ #end if #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": +#if $track.track_file_style_conditional.spacer_height != "": [spacer] -#if $track.track_file_style_conditional.spacer_height: height = $track.track_file_style_conditional.spacer_height #end if #end if @@ -366,25 +444,20 @@ <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"/> + <expand macro="minmax_macro" /> <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> + <option value="">no transformation</option> </param> - <param name="height_matrix" type="float" value="1.5" optional="True" label="height"/> - - <param name="type" type="select" optional="True" label="Plotting type"> - <option value="arcplot">arcplot</option> - <option value="interaction">interaction</option> - </param> + <param name="height_matrix" type="float" value="" optional="True" label="height"/> <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show masked bins" /> <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple='True'/> <!-- multiple='True'--> <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" /> - <param name="x_labels" type="boolean" truevalue="yes" falsevalue="no" optional="True" label="Show x labels" /> + <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> </when> @@ -404,26 +477,27 @@ <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" /> + <expand macro="color_bed_macro" /> <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Plot labels" /> <expand macro="spacer_macro" /> - + </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" /> + <expand macro="track_input_bed_gtf_macro" /> + <expand macro="color_bed_macro" /> <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Plot labels" /> - <param name="type" type="select" optional="True" label="Type"> - <option value="genes">genes</option> - <option value="domains">domains</option> + <param name="flybase" type="boolean" checked="true" label="Use flybase style" help="This will be only used for bed with 12 columns"/> + <param name="display" type="select" label="display to use"> + <option value="stacked" selected="True">stacked (no overlap even with the label)</option> + <option value="interlaced">interlaced (everything on 2 lines)</option> + <option value="collapsed">collapsed (everything on 1 line)</option> + <option value="domain">domain (only the first line of stacked)</option> </param> <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Global max rows" /> @@ -435,10 +509,13 @@ <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="height_bedgraph" type="float" value="0.2" optional="True" label="height"/> + <expand macro="color_coverage_macro" /> + <expand macro="minmax_macro" /> + <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> + <expand macro="type_coverage_macro" /> <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> + <expand macro="inverted_macro" /> + <expand macro="overlay_macro" /> <expand macro="spacer_macro" /> </when> @@ -446,30 +523,17 @@ <expand macro="plot_title" /> <expand macro="track_input_bigwig_macro" /> - <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> + <expand macro="color_coverage_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"/> + <expand macro="minmax_macro" /> <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> - <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"> - <param name="type_selector" type="select" label="Choose style of the plot."> - <option value="fill_option">fill</option> - <option value="line_option">line</option> - <option value="point_option">point</option> - </param> - <when value="line_option"> - <param name="width_line" type="float" value="0.5" optional="True" label="Width"/> - </when> - <when value="point_option"> - <param name="width_point" type="float" value="0.5" optional="True" label="Width"/> - </when> - <when value="fill_option" /> - </conditional> - <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" /> + <expand macro="reading_bw_macro" /> + <expand macro="type_coverage_macro" /> + <expand macro="type_coverage_macro" /> + <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" label="Show visualization of data range"/> + <expand macro="inverted_macro" /> + <expand macro="overlay_macro" /> <expand macro="spacer_macro" /> </when> @@ -479,14 +543,14 @@ <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"/> + <expand macro="minmax_macro" /> <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> - <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" + <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"/> + <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> </when> @@ -508,8 +572,8 @@ </param> <when value="yes"> <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> - <param name="where" type="select" optional="True" label="Where to place the x-axis"> - <option value="top" >Top</option> + <param name="where" type="select" label="Where to place the x-axis"> + <option value="top" selected="True">Top</option> <option value="bottom">Bottom</option> </param> </when> @@ -538,7 +602,6 @@ <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hic_matrix_option" /> <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> - <param name="title" value="Kc DpnII (Li et al. 2015)" /> <param name="colormap" value="RdYlBu_r" /> <param name="depth" value="200000" /> @@ -560,6 +623,9 @@ <param name="title" value="TAD state" /> <param name="height_chrom" value="0.5" /> <param name="labels" value="off" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="bed_rgb" /> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -597,7 +663,6 @@ </conditional> </conditional> </repeat> - <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> @@ -611,7 +676,6 @@ </conditional> </conditional> </repeat> - <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> @@ -626,7 +690,6 @@ </conditional> </conditional> </repeat> - <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> @@ -641,7 +704,6 @@ </conditional> </conditional> </repeat> - <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="spacer_option" /> @@ -678,7 +740,7 @@ <param name="track_file_style_selector" value="spacer_option" /> <param name="spacer_height" value="1" /> </conditional> - </repeat> + </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> @@ -700,34 +762,271 @@ <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> </test> <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="bigwig_track_option" /> - <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> - <param name="title" value="rep 1 test line" /> - <param name="height_bigwig" value="4" /> - <param name="color" value="red" /> - <conditional name="type_conditional"> - <param name="type_selector" value="line_option" /> - <param name="width_line" value="1" /> + <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="bigwig_track_option" /> + <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> + <param name="title" value="rep 1 test line" /> + <param name="height_bigwig" value="4" /> + <param name="color" value="red" /> + <conditional name="type_conditional"> + <param name="type_selector" value="line_option" /> + <param name="width_line" value="1" /> + </conditional> </conditional> - </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <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_multiple" value="Li_et_al_2015.h5"/> + <param name="title" value="Kc DpnII (Li et al. 2015) log1p" /> + <param name="colormap" value="RdYlBu_r" /> + <param name="depth" value="200000" /> + <param name="transform" value="log1p" /> + <param name="boundaries_file" value="domains.bed" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <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="height_chrom" value="0.5" /> + <param name="labels" value="off" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="bed_rgb" /> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="hic_matrix_option" /> + <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> + <param name="title" value="Kc DpnII (Li et al. 2015) inverted no transform" /> + <param name="colormap" value="Reds" /> + <param name="depth" value="200000" /> + <param name="transform" value="" /> + <param name="invert_orientation" value="yes" /> + <param name="min_value" value="5" /> + <param name="max_value" value="70" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="spacer_option" /> + <param name="spacer_height" value="1" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="test_with_neg_values.bg.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph with negative values" /> + <param name="height_bedgraph" value="4" /> + <param name="color" value="black" /> + <conditional name="color_negative"> + <param name="color_negative_select" value="yes" /> + <param name="color" value="red" /> + </conditional> + <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="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> + <param name="title" value="bedgraph" /> + <param name="height_bedgraph" 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 fill" /> + <param name="height_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="(red points/width=5/max value/100 bins) overlayed with (dark red line/min value/30000 bins) overlayed with (black line/min value)" /> + <param name="height_bigwig" value="10" /> + <param name="color" value="red" /> + <conditional name="type_conditional"> + <param name="type_selector" value="point_option" /> + <param name="width_point" value="5" /> + </conditional> + <section name="reading_bw_conditional"> + <param name="summary" value="max"/> + <param name="number_of_bins" value="100"/> + </section> + </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="height_bigwig" value="10" /> + <param name="color" value="#c00000" /> + <conditional name="type_conditional"> + <param name="type_selector" value="line_option" /> + </conditional> + <section name="reading_bw_conditional"> + <param name="summary" value="min"/> + </section> + <param name="overlay_select" value="share-y" /> + </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="height_bigwig" value="10" /> + <param name="color" value="black" /> + <conditional name="type_conditional"> + <param name="type_selector" value="line_option" /> + </conditional> + <section name="reading_bw_conditional"> + <param name="summary" value="min"/> + <param name="number_of_bins" value="30000"/> + </section> + <param name="overlay_select" value="share-y" /> + <param name="spacer_height" value="1" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <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 in ucsc" /> + <param name="height_bed" value="5" /> + <param name="fontsize" value="10" /> + <param name="flybase" value="false"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> + <param name="title" value="bed6 global max row color from score" /> + <param name="height_bed" value="20" /> + <param name="fontsize" value="10" /> + <param name="global_max_row" value="True" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="colormap" /> + <param name="color" value="RdYlBu_r" /> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <param name="track_input_bed" value="domains.bed" ftype="bed" /> + <param name="title" value="domains.bed using the 9th field for colors interlaced" /> + <param name="height_bed" value="2" /> + <param name="fontsize" value="10" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="bed_rgb" /> + </conditional> + <param name="display" value="interlaced" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" /> + </test> + <test> + <param name="region" value="X:2700000-3100000"/> + <conditional name="x_axis"> + <param name="x_axis_select" value="yes" /> + <param name="where" value="bottom" /> + </conditional> + <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="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" /> + <param name="height_bigwig" value="7" /> + <param name="color" value="#00b0f0" /> + <param name="number_of_bins" value="2000"/> + </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="" /> + <param name="color" value="#ff0000" /> + <param name="alpha" value="0.5" /> + <param name="summary" value="max" /> + <param name="number_of_bins" value="300"/> + <param name="overlay_select" value="share-y"/> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" /> + </test> + <test> + <param name="region" value="X:3000000-3300000"/> + <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="gene_track_option" /> + <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> + <param name="title" value="test" /> + <param name="height_bed" value="10" /> + <param name="color" value="#000000" /> + <param name="flybase" value="false" /> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="gene_track_option" /> + <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> + <param name="title" value="test" /> + <param name="height_bed" value="10" /> + <param name="color" value="#000000" /> + <param name="flybase" value="false" /> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" /> + </test> </tests> <help><![CDATA[ pyGenomeTracks ============== -**pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable. - Currently, it is possible to plot: +**pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable. + Currently, it is possible to plot: - bigwig - bed (many options) @@ -761,12 +1060,12 @@ Output ------ -**pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) +**pyGenomeTracks** 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 **pyGenomeTracks**. -TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to: -TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states, -principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. +TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to: +TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states, +principal component 1 (A/B compartment) computed using HiCExplorer's ``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/pyGenomeTracks.png