Mercurial > repos > iuc > pygenometracks
changeset 7:326a3db8d9d1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
| author | iuc |
|---|---|
| date | Fri, 17 Apr 2020 11:57:44 -0400 |
| parents | 5cec5fb749f0 |
| children | 4ac4e7083b7e |
| files | macros.xml pyGenomeTracks.xml test-data/dm3_genes_withrgbandscore.bed.gz test-data/master_TADs_BW_plot.png test-data/master_TADs_plot.png test-data/test13.ini test-data/test14.ini test-data/test15.ini test-data/test3.ini test-data/test6.ini test-data/test7.ini test-data/test_arrowhead_zoom.png test-data/test_gtf_bed4.png test-data/test_gtf_flybase_param.png test-data/test_link2.png test-data/test_narrowPeak.png test-data/test_scale_bar.png test-data/test_tssarrow.png test-data/test_ucsc_param.png test-data/testpyGT.sh |
| diffstat | 20 files changed, 1202 insertions(+), 686 deletions(-) [+] |
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--- a/macros.xml Tue Feb 11 10:20:24 2020 -0500 +++ b/macros.xml Fri Apr 17 11:57:44 2020 -0400 @@ -1,6 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">3.2.1</token> + <token name="@WRAPPER_VERSION@">3.3</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement> @@ -15,159 +15,6 @@ <yield /> </citations> </xml> - - <xml name="colormap"> - <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" 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> - </xml> - - <xml name="region"> - <param argument="--region" type="text" label="Region of the genome to limit the operation" - help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" /> - </xml> - - <xml name="matrix_h5_cooler_multiple_macro"> - <param name="matrix_h5_cooler_multiple" type="data" format="h5,cool" - label="Matricies to compute on" multiple="true"/> - </xml> <token name="@REFERENCES@"> .. class:: infomark @@ -184,31 +31,36 @@ .. _help site: https://github.com/deeptools/pyGenomeTracks </token> - + <!-- all input files--> + <xml name="matrix_h5_cooler_multiple_macro"> + <param name="matrix_h5_cooler_multiple" type="data" format="h5,cool" + label="Matricies to plot" multiple="true"/> + </xml> <xml name="track_input_bed_macro"> - <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple="True"/> + <param name="track_input_bed" type="data" format="bed" label="Track file(s) 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"/> + <param name="track_input_bed" type="data" format="bed,gtf" label="Track file(s) bed or gtf format" multiple="True"/> </xml> <xml name="track_input_narrow_peak_macro"> - <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file encodepeak or format" multiple="True"/> + <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file(s) encodepeak or bed 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> <xml name="track_input_bedgraph_macro"> - <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" multiple="True"/> + <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file(s) bedgraph format" multiple="True"/> </xml> <xml name="track_input_bigwig_macro"> - <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" multiple="True"/> + <param name="track_input_bigwig" type="data" format="bigwig" label="Track file(s) bigwig format" multiple="True"/> </xml> <xml name="track_input_bedgraph_matrix_macro"> - <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" multiple="True"/> + <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file(s) bedgraph format" multiple="True"/> </xml> <xml name="track_input_link_macro"> - <param name="track_input_link" type="data" format="bed,interval" label="Track file for links" multiple="False"/> + <param name="track_input_link" type="data" format="bed,interval" label="Track file(s) for links" multiple="False"/> </xml> + <!-- Common to nearly all tracks: --> <xml name="plot_title"> <param name="title" type="text" optional="true" label="Plot title" multiple="True"/> </xml> @@ -220,162 +72,18 @@ <param name="invert_orientation" type="boolean" truevalue="true" falsevalue="false" 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 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="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> + <!-- More specific but still present twice:--> <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"/> @@ -390,13 +98,6 @@ </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."> @@ -413,46 +114,48 @@ <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> + <xml name="border_color_bed_macro"> + <conditional name="border_color_bed"> + <param name="border_color_bed_select" type="select" label="Define border color:"> + <option value="manually" selected="True">manually</option> + <option value="bed_rgb">From the 9th field</option> + <option value="none">No border</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> + <when value="manually"> + <param name="color" type="color" value="#000000" label="Color of the border"/> + </when> + <when value="bed_rgb" /> + <when value="none" /> + </conditional> </xml> <xml name="bed_advanced_macro"> - <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> - <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false" - label="Global max rows" /> - <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" /> - <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" /> - <param name="line_width" type="float" value="0.5" label="width of lines" /> - <section name ="flybase" title="When using flybase style" expanded="False"> - <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions in flybase style"/> - <param name="color_utr" type="color" value="grey" label="Color of UTR regions"/> - </section> - <section name ="ucsc" title="When using UCSC style" expanded="False"> - <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/> - </section> - <section name ="gtf" title="When using gtf as input" expanded="False"> - <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label" - help="Usually transcript_name or gene_name"/> - <param name="merge_transcripts" type="boolean" truevalue="true" falsevalue="false" checked="false" - label="Merge all transcripts of each gene in a single entry" /> - </section> + <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Global max rows" /> + <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" /> + <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" /> + <param name="line_width" type="float" value="0.5" label="width of lines" /> + <section name ="gtf" title="When using gtf as input" expanded="False"> + <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label" + help="Usually transcript_name or gene_name"/> + <param name="merge_transcripts" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Merge all transcripts of each gene in a single entry" /> </section> </xml> + <xml name="utr_macro"> + <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions"/> + <conditional name="color_utr"> + <param name="color_utr_select" type="select" label="Define UTR color:"> + <option value="manually" selected="True">manually</option> + <option value="bed_rgb">From the 9th field</option> + <option value="like">Like the coding</option> + </param> + <when value="manually"> + <param name="color" type="color" value="grey" label="Color of UTR regions"/> + </when> + <when value="bed_rgb" /> + <when value="like" /> + </conditional> + </xml> <xml name="lines_macro"> <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"/> <param name="line_width" type="float" value="0.5" label="width of line(s)" optional="True"/> @@ -463,157 +166,154 @@ <option value="dashdot">Dashdot</option> </param> </xml> - <xml name="links_color_macro"> - <conditional name="color_link"> - <param name="color_link_select" type="select" label="Use color:"> - <option value="manually" selected="True">manually</option> - <option value="colormap">From the 7th field (score)</option> - </param> - <when value="manually"> - <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> - </when> - <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> + <xml name="colormap_macro"> + <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="viridis">viridis</option> + <option value="plasma">plasma</option> + <option value="inferno">inferno</option> + <option value="magma">magma</option> + <option value="cividis">cividis</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">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> + <option value="viridis_r">viridis reversed</option> + <option value="plasma_r">plasma reversed</option> + <option value="inferno_r">inferno reversed</option> + <option value="magma_r">magma reversed</option> + <option value="cividis_r">cividis reversed</option> </xml> </macros>
--- a/pyGenomeTracks.xml Tue Feb 11 10:20:24 2020 -0500 +++ b/pyGenomeTracks.xml Fri Apr 17 11:57:44 2020 -0400 @@ -30,24 +30,20 @@ #if $region and $region is not None: --region '$region' #end if + #if $global_args.title is not None: + --title '$global_args.title' + #end if + --fontSize $global_args.fontsize + --dpi $global_args.dpi + --trackLabelFraction $global_args.trackLabelFraction + --trackLabelHAlign $global_args.trackLabelHAlign --outFileName plot.$image_file_format && mv plot.$image_file_format plot ]]> </command> <configfiles> <configfile name="tracks_config"> -## First the xaxis if where = top -#if $x_axis.x_axis_select == "true": - #if $x_axis.where == 'top': -[x-axis] - #if $x_axis.fontsize: -fontsize = $x_axis.fontsize - #end if -where = top - #end if -#end if - -## Then each track: +## Each track: #for $counter, $track in enumerate($tracks): ## Hi-C Track #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": @@ -124,8 +120,10 @@ #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 + #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': +border_color = $track.track_file_style_conditional.border_color_bed.color + #else +border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select #end if display = collapsed #if $track.track_file_style_conditional.height_chrom: @@ -148,8 +146,8 @@ #set ext = $data_bed.extension file = ${counter}_${counter_bed}.$ext #if $ext == 'gtf': -prefered_name = $track.track_file_style_conditional.bed_advanced.gtf.prefered_name -merge_transcripts = $track.track_file_style_conditional.bed_advanced.gtf.merge_transcripts +prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name +merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts #end if #if $track.track_file_style_conditional.title: title = $track.track_file_style_conditional.title @@ -161,33 +159,53 @@ #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 + #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': +border_color = $track.track_file_style_conditional.border_color_bed.color + #else +border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select #end if - #if $track.track_file_style_conditional.flybase: -style = flybase -height_utr = $track.track_file_style_conditional.bed_advanced.flybase.height_utr -color_utr = $track.track_file_style_conditional.bed_advanced.flybase.color_utr - #else -style = UCSC -arrow_interval = $track.track_file_style_conditional.bed_advanced.ucsc.arrow_interval +style = $track.track_file_style_conditional.bed_style.bed_style_select + #if $track.track_file_style_conditional.bed_style.bed_style_select == 'UCSC': +arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval + #else: +height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr + #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'manually': +color_utr = $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color + #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb': +color_utr = bed_rgb + #else: + #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": +color_utr = bed_rgb + #else: +color_utr = $track.track_file_style_conditional.color_bed.color + #end if + #end if + #if $track.track_file_style_conditional.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length != '': +arrow_length = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length + #end if + #if $track.track_file_style_conditional.bed_style.bed_style_select == 'flybase': +arrowhead_included = $track.track_file_style_conditional.bed_style.arrowhead_included + #end if #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 -labels = $track.track_file_style_conditional.labels +labels = $track.track_file_style_conditional.labels.plot_labels + #if $track.track_file_style_conditional.labels.plot_labels == 'true': +all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside +labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin + #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.bed_advanced.gene_rows: -gene_rows = $track.track_file_style_conditional.bed_advanced.gene_rows + #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows: +gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows #end if -global_max_row = $track.track_file_style_conditional.bed_advanced.global_max_row -max_labels = $track.track_file_style_conditional.bed_advanced.max_labels -line_width = $track.track_file_style_conditional.bed_advanced.line_width -arrowhead_included = $track.track_file_style_conditional.arrowhead_included +global_max_row = $track.track_file_style_conditional.bed_style.bed_advanced.global_max_row +max_labels = $track.track_file_style_conditional.bed_style.bed_advanced.max_labels +line_width = $track.track_file_style_conditional.bed_style.bed_advanced.line_width #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if @@ -223,6 +241,10 @@ line_width = $track.track_file_style_conditional.line_width line_style = $track.track_file_style_conditional.line_style links_type = $track.track_file_style_conditional.links_type +compact_arcs_level = $track.track_file_style_conditional.compact_arcs_level + #if $track.track_file_style_conditional.ylim != "": +ylim = $track.track_file_style_conditional.ylim + #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if @@ -263,6 +285,7 @@ #if $track.track_file_style_conditional.height_narrow_peak: height = $track.track_file_style_conditional.height_narrow_peak #end if +line_width = $track.track_file_style_conditional.line_width show_labels = $track.track_file_style_conditional.show_labels file_type = narrow_peak #if $track.track_file_style_conditional.fontsize: @@ -404,13 +427,15 @@ #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.type_lines: -type = $track.track_file_style_conditional.type_lines - #end if +type = $track.track_file_style_conditional.type.type_selector file_type = bedgraph_matrix -show_data_range = $track.track_file_style_conditional.show_data -plot_horizontal_lines = $track.track_file_style_conditional.plot_horizontal_lines -pos_score_in_bin = $track.track_file_style_conditional.pos_score_in_bin + #if $track.track_file_style_conditional.type.type_selector == 'lines': +show_data_range = $track.track_file_style_conditional.type.show_data +plot_horizontal_lines = $track.track_file_style_conditional.type.plot_horizontal_lines +pos_score_in_bin = $track.track_file_style_conditional.type.pos_score_in_bin + #else +colormap = $track.track_file_style_conditional.type.colormap + #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if @@ -465,28 +490,83 @@ ## Spacer #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": [spacer] + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #end if #if $track.track_file_style_conditional.spacer_height != "": height = $track.track_file_style_conditional.spacer_height #end if #end if + + ## Xaxis: + #if $track.track_file_style_conditional.track_file_style_selector == "xaxis_option": +[x-axis] + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #end if + #if $track.track_file_style_conditional.fontsize != "": +fontsize = $track.track_file_style_conditional.fontsize + #end if +where = $track.track_file_style_conditional.xaxis_where + ## If spacer is asked a new section is created: + #if $track.track_file_style_conditional.spacer_height != "": +[spacer] +height = $track.track_file_style_conditional.spacer_height + #end if + #end if + + ## Scale bar: + #if $track.track_file_style_conditional.track_file_style_selector == "scale_bar_option": +[scale_bar] + #if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title + #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 +line_width = $track.track_file_style_conditional.line_width + #if $track.track_file_style_conditional.x_center != "": +x_center = $track.track_file_style_conditional.x_center + #end if + #if $track.track_file_style_conditional.size != "": +size = $track.track_file_style_conditional.size + #end if +where = $track.track_file_style_conditional.sb_where + #if $track.track_file_style_conditional.fontsize != "": +fontsize = $track.track_file_style_conditional.fontsize + #end if +file_type = scalebar + ## If spacer is asked a new section is created: + #if $track.track_file_style_conditional.spacer_height != "": +[spacer] +height = $track.track_file_style_conditional.spacer_height + #end if + #end if #end for - -#if $x_axis.x_axis_select == "true": - #if $x_axis.where == 'bottom': -[x-axis] - #if $x_axis.fontsize: -fontsize = $x_axis.fontsize - #end if -where = bottom - #end if -#end if </configfile> </configfiles> <inputs> - <expand macro="region" /> - + <!--Arguments for pgt--> + <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false" + help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" /> + <section name="global_args" title="Configure figure parameters" expanded="False"> + <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/> + <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/> + <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72" + help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/> + <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05" + min="0" max="1"/> + <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels"> + <option value="left" selected="True">left</option> + <option value="right">right</option> + <option value="center">center</option> + </param> + </section> + <!--Info to build the config file--> <repeat name="tracks" min="1" title="Include tracks in your plot" - help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph"> + help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph. + The order you add them represent the order they will be plotted from top to bottom."> <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> @@ -501,12 +581,17 @@ <option value="vlines_track_option">Vlines track</option> <option value="hlines_track_option">Hlines track</option> <option value="spacer_option">Spacer</option> + <option value="xaxis_option">X-axis</option> + <option value="scale_bar_option">Scale bar track</option> </param> <when value="hic_matrix_option"> <expand macro="plot_title" /> <expand macro="matrix_h5_cooler_multiple_macro" /> - <expand macro="colormap" /> + <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> + <option value="RdYlBu_r">RdYlBu reversed</option> + <expand macro="colormap_macro"/> + </param> <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> <expand macro="minmax_macro" /> <param name="transform" type="select" label="Plot the transformed value"> @@ -530,7 +615,23 @@ <when value="chrom_states_option"> <expand macro="plot_title" /> <expand macro="track_input_bed_macro" /> - <expand macro="color_bed_macro" /> + <conditional name="color_bed"> + <param name="color_bed_select" type="select" label="Define 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"> + <expand macro="colormap_macro" /> + </param> + </when> + </conditional> + <expand macro="border_color_bed_macro" /> <param name="line_width" type="float" value="0.5" label="width of lines" /> <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true" @@ -542,22 +643,75 @@ <expand macro="plot_title" /> <expand macro="track_input_bed_gtf_macro" /> - <expand macro="color_bed_macro" /> + <conditional name="color_bed"> + <param name="color_bed_select" type="select" label="Define 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"> + <expand macro="colormap_macro" /> + </param> + </when> + </conditional> + <expand macro="border_color_bed_macro" /> <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> - <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true" - label="Plot labels" /> - <param name="flybase" type="boolean" checked="true" label="Use flybase style" help="This will be only used for bed with 12 columns"/> + <conditional name="labels"> + <param name="plot_labels" type="select" label="Plot labels"> + <option value="true" selected="True">yes</option> + <option value="false">no</option> + </param> + <when value="true"> + <param name="all_labels_inside" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Put all labels inside the plotted region" + help="Put labels on the left of the region if the region ends after the plotted region."/> + <param name="labels_in_margin" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Allow to put labels in the right margin" + help="Put labels in the margin if the region ends after the plotted region."/> + </when> + <when value="false"/> + </conditional> <param name="display" type="select" label="display to use"> <option value="stacked" selected="True">stacked (no overlap even with the label)</option> <option value="interleaved">interleaved (everything on 2 lines)</option> <option value="collapsed">collapsed (everything on 1 line)</option> <option value="triangles">triangles (plot triangles between start and end)</option> </param> - <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false" - label="Include the arrowhead in the bed interval:" - help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/> <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> - <expand macro="bed_advanced_macro" /> + <conditional name="bed_style"> + <param name="bed_style_select" type="select" label="Bed style"> + <option value="flybase" selected="True">flybase (blocks with arrow at extremities)</option> + <option value="UCSC">UCSC (blocks with arrows in introns)</option> + <option value="tssarrow">tssarrow (blocks with arrow above at beginning)</option> + </param> + <when value="flybase"> + <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Include the arrowhead in the bed interval:" + help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/> + <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> + <expand macro="utr_macro" /> + <expand macro="bed_advanced_macro" /> + </section> + </when> + <when value="UCSC"> + <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> + <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/> + <expand macro="bed_advanced_macro" /> + </section> + </when> + <when value="tssarrow"> + <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> + <param name="arrow_length" type="integer" optional="true" label="arrow length" help="the length of the arrow in bp (default is 4% of the plotted region)"/> + <expand macro="utr_macro" /> + <expand macro="bed_advanced_macro" /> + </section> + </when> + </conditional> <expand macro="overlay_macro" /> <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> @@ -566,13 +720,32 @@ <when value="link_track_option"> <expand macro="plot_title" /> <expand macro="track_input_link_macro" /> - <expand macro="links_color_macro" /> + <conditional name="color_link"> + <param name="color_link_select" type="select" label="Define color:"> + <option value="manually" selected="True">manually</option> + <option value="colormap">From the 7th field (score)</option> + </param> + <when value="manually"> + <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> + </when> + <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"> + <expand macro="colormap_macro" /> + </param> + </when> + </conditional> <expand macro="lines_macro" /> <param name="links_type" type="select" label="Representation of the link:"> <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option> <option value="triangles">triangles</option> <option value="loops">loops (a rectangle highlighting the intersection)</option> </param> + <param name="compact_arcs_level" type="select" label="Height of arcs and triangles:"> + <option value="0" selected="True">default (proportional to distance)</option> + <option value="1">compacted (the height is proportional to the square root of the distance)</option> + <option value="2">highly compacted (the height is the same for all distances)</option> + </param> + <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/> <param name="height" type="float" value="1.5" optional="True" label="height"/> <expand macro="minmax_macro" /> <expand macro="overlay_macro" /> @@ -603,6 +776,7 @@ optional="True" label="Plot a vertical bar at the summit position." /> </when> </conditional> + <param name="line_width" type="float" value="1" label="width of lines" /> <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Plot labels (name, p-val, q-val)" /> <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> @@ -636,8 +810,18 @@ <expand macro="minmax_macro" /> <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> - <expand macro="reading_bw_macro" /> - <expand macro="type_coverage_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> <expand macro="type_coverage_macro" /> <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> <expand macro="inverted_macro" /> @@ -654,15 +838,30 @@ <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> - <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."/> - <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end" help="Only used when type is lines"> - <option value="center" selected="True">Center</option> - <option value="block">Block (draw a horizontal line between start and end)</option> - </param> - <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Plot an horizontal line at 0 when type is lines" /> - <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" /> + <conditional name="type"> + <param name="type_selector" type="select" label="type of plotting"> + <option value="lines" selected="True">lines: each column in the bedgraph will be a line and a mean line will be added</option> + <option value="matrix">matrix: each column in the bedgraph will be a raw in the matrix</option> + </param> + <when value="lines"> + <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Plot an horizontal line at 0 when type is lines" /> + <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" + label="Show visualization of data range" /> + <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end"> + <option value="center" selected="True">Center</option> + <option value="block">Block (draw a horizontal line between start and end)</option> + </param> + </when> + <when value="matrix"> + <param name="colormap" type="select" label="colormap"> + <option value="viridis">Viridis</option> + <expand macro="colormap_macro" /> + </param> + </when> + </conditional> + + <expand macro="inverted_macro" /> <expand macro="spacer_macro" /> @@ -683,28 +882,41 @@ <expand macro="spacer_macro" /> </when> <when value="spacer_option"> + <expand macro="plot_title" /> <param name="spacer_height" type="float" value="" optional="True" label="Height of the spacer."/> </when> + <when value="xaxis_option"> + <expand macro="plot_title" /> + <param name="fontsize" type="float" optional="True" + label="Fontsize of the x-axis."/> + <param name="xaxis_where" type="select" label="chromosome name and coordinates position relative to the axis"> + <option value="bottom" selected="True">below</option> + <option value="top">above</option> + </param> + <expand macro="spacer_macro" /> + </when> + <when value="scale_bar_option"> + <expand macro="plot_title" /> + <param name="color" type="color" label="Color of the scale bar" 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"/> + <param name="line_width" type="float" value="0.5" label="width of lines"/> + <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True" + help="If not set it will be in the middle of the plotted area."/> + <param name="size" type="integer" label="size of the scale bar" optional="True" + help="If not set it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/> + <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar"> + <option value="left" selected="True">left</option> + <option value="right">right</option> + <option value="bottom">below</option> + <option value="top">above</option> + </param> + <param name="fontsize" type="float" optional="True" + label="Fontsize of the size of the scale bar."/> + <expand macro="spacer_macro" /> + </when> </conditional> - </repeat> - - - <conditional name="x_axis"> - <param name="x_axis_select" type="select" label="Configure x-axis"> - <option value="false" selected="True">No</option> - <option value="true">Yes</option> - </param> - <when value="true"> - <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> - <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> - <when value="false" /> - </conditional> <param name="image_file_format" type="select" label="Image output format"> <option value="png">png</option> <option value="svg">svg</option> @@ -719,17 +931,21 @@ </data> </outputs> <tests> + <!--test 1--> <test> <param name="region" value="chrX:3000000-3500000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="top" /> + </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)" /> - <param name="colormap" value="RdYlBu_r" /> + <!--<param name="colormap" value="RdYlBu_r" />--> <param name="depth" value="200000" /> <param name="transform" value="log1p" /> <param name="boundaries_file" value="domains.bed" /> @@ -758,6 +974,10 @@ <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> <param name="title" value="TAD separation score (Ramirez et al.)" /> + <conditional name="type"> + <param name="type_selector" value="matrix" /> + <!--<param name="colormap" value="viridis" />--> + </conditional> <param name="height_bedgraph" value="10" /> </conditional> </repeat> @@ -857,9 +1077,11 @@ <param name="title" value="max num rows 3" /> <param name="height_bed" value="3" /> <param name="fontsize" value="8" /> - <section name="bed_advanced"> - <param name="gene_rows" value="3" /> - </section> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="gene_rows" value="3" /> + </section> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -875,9 +1097,11 @@ <param name="title" value="bed6 global max row" /> <param name="height_bed" value="20" /> <param name="fontsize" value="10" /> - <section name="bed_advanced"> - <param name="global_max_row" value="true" /> - </section> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="global_max_row" value="true" /> + </section> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -889,11 +1113,15 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 2--> <test> <param name="region" value="chrX:3000000-3500000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="top" /> + </conditional> + </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="bigwig_track_option" /> @@ -949,11 +1177,15 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 3--> <test> <param name="region" value="chrX:3000000-3500000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="top" /> + </conditional> + </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hic_matrix_option" /> @@ -1092,7 +1324,9 @@ <param name="title" value="genes in ucsc" /> <param name="height_bed" value="5" /> <param name="fontsize" value="10" /> - <param name="flybase" value="false"/> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -1102,9 +1336,11 @@ <param name="title" value="bed6 global max row color from score" /> <param name="height_bed" value="20" /> <param name="fontsize" value="10" /> - <section name="bed_advanced"> - <param name="global_max_row" value="true" /> - </section> + <conditional name="bed_style"> + <section name="bed_advanced"> + <param name="global_max_row" value="true" /> + </section> + </conditional> <conditional name="color_bed"> <param name="color_bed_select" value="colormap" /> <param name="color" value="RdYlBu_r" /> @@ -1115,26 +1351,66 @@ <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 interleaved" /> + <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" /> + <param name="height_bed" value="2" /> + <param name="fontsize" value="10" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="bed_rgb" /> + </conditional> + <conditional name="border_color_bed"> + <param name="border_color_bed_select" value="manually" /> + <param name="color" value="red" /> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="false" /> + </conditional> + <param name="display" value="interleaved" /> + </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 interleaved border=bed_rgb" /> <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="border_color" value="red" /> - <param name="labels" value="false" /> + <conditional name="border_color_bed"> + <param name="border_color_bed_select" value="bed_rgb" /> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="false" /> + </conditional> + <param name="display" value="interleaved" /> + </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 interleaved border=none" /> + <param name="height_bed" value="2" /> + <param name="fontsize" value="10" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="bed_rgb" /> + </conditional> + <conditional name="border_color_bed"> + <param name="border_color_bed_select" value="none" /> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="false" /> + </conditional> <param name="display" value="interleaved" /> </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 4--> <test> <param name="region" value="X:2700000-3100000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - <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" /> @@ -1161,14 +1437,24 @@ <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="xaxis_option" /> + <param name="xaxis_where" value="bottom" /> + </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 5--> <test> <param name="region" value="X:3000000-3300000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="top" /> + </conditional> + </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> @@ -1176,7 +1462,9 @@ <param name="title" value="test" /> <param name="height_bed" value="10" /> <param name="color" value="#000000" /> - <param name="flybase" value="false" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + </conditional> <param name="spacer_height" value="1"/> </conditional> </repeat> @@ -1187,19 +1475,18 @@ <param name="title" value="test" /> <param name="height_bed" value="10" /> <param name="color" value="#000000" /> - <param name="flybase" value="false" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + </conditional> <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> + <!--test 6--> <test> <param name="region" value="X:2760000-2802000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - <param name="where" value="bottom" /> - </conditional> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="narrow_peak_track_option" /> @@ -1217,6 +1504,21 @@ <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="narrow_peak_track_option" /> + <param name="title" value="box line_width = 2" /> + <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> + <param name="color" value="#9bbb59" /> + <param name="height_narrow_peak" value="4" /> + <param name="line_width" value="2" /> + <conditional name="display"> + <param name="display_selector" value="box" /> + <param name="use_summit" value="true" /> + </conditional> + <param name="show_labels" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="narrow_peak_track_option" /> <param name="title" value="peak width 3" /> <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> <param name="color" value="#c0504d" /> @@ -1247,14 +1549,24 @@ <param name="show_labels" value="true" /> </conditional> </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="bottom" /> + </conditional> + </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 7--> <test> <param name="region" value="chrX:3300000-3500000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="top" /> + </conditional> + </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> @@ -1269,37 +1581,110 @@ <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> <param name="title" value="gtf" /> <param name="height_bed" value="10" /> - <section name="bed_advanced"> - <section name ="flybase"> + <conditional name="bed_style"> + <section name="bed_advanced"> <param name="height_utr" value="0.75"/> - <param name="color_utr" value="#ff0000"/> + <conditional name="color_utr"> + <param name="color_utr_select" value="manually"/> + <param name="color" value="#ff0000"/> + </conditional> + <section name ="gtf"> + <param name="prefered_name" value="gene_name"/> + <param name="merge_transcripts" value="true"/> + </section> + </section> + </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="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + <param name="title" value="genes with scores" /> + <param name="height_bed" value="10" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="colormap" /> + <param name="color" value="cool_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="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + <param name="title" value="genes with utr as bed_rgb" /> + <param name="height_bed" value="10" /> + <conditional name="bed_style"> + <section name="bed_advanced"> + <conditional name="color_utr"> + <param name="color_utr_select" value="bed_rgb"/> + </conditional> </section> - <section name ="gtf"> - <param name="prefered_name" value="gene_name"/> - <param name="merge_transcripts" value="true"/> + </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="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + <param name="title" value="genes with coding as bed_rgb - labels_in_margin" /> + <param name="height_bed" value="10" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="bed_rgb" /> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="true" /> + <param name="labels_in_margin" value="true" /> + </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="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> + <param name="title" value="genes bed_rgb like - all_labels_inside" /> + <param name="height_bed" value="10" /> + <conditional name="color_bed"> + <param name="color_bed_select" value="bed_rgb" /> + </conditional> + <conditional name="bed_style"> + <section name="bed_advanced"> + <conditional name="color_utr"> + <param name="color_utr_select" value="like"/> + </conditional> </section> - </section> + </conditional> + <conditional name="labels"> + <param name="plot_labels" value="true" /> + <param name="all_labels_inside" value="true" /> + </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 8--> <test> <param name="region" value="chrX:3300000-3500000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="top" /> + </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="dm3_genes.bed" /> <param name="height_bed" value="10" /> - <param name="flybase" value="false" /> - <section name="bed_advanced"> - <param name="global_max_row" value="true" /> - <param name="max_labels" value="15" /> - </section> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + <section name="bed_advanced"> + <param name="global_max_row" value="true" /> + <param name="max_labels" value="15" /> + </section> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -1308,30 +1693,33 @@ <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> <param name="title" value="genes.bed.gz" /> <param name="height_bed" value="10" /> - <param name="flybase" value="false" /> - <section name="bed_advanced"> - <param name="line_width" value="2"/> - <section name ="ucsc"> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + <section name="bed_advanced"> <param name="arrow_interval" value="10"/> + <param name="line_width" value="2"/> </section> - </section> + </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 9--> <test> <param name="region" value="X:3133000-3138000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="top" /> + </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.gtf.gz" ftype="gtf" /> <param name="title" value="test" /> <param name="height_bed" value="10" /> - <param name="flybase" value="true" /> <param name="spacer_height" value="1"/> </conditional> </repeat> @@ -1345,7 +1733,9 @@ <param name="color_bed_select" value="manually" /> <param name="color" value="red" /> </conditional> - <param name="flybase" value="false" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + </conditional> <param name="spacer_height" value="1"/> </conditional> </repeat> @@ -1359,9 +1749,10 @@ <param name="color_bed_select" value="manually" /> <param name="color" value="red" /> </conditional> - <param name="flybase" value="true" /> <param name="spacer_height" value="1"/> - <param name="arrowhead_included" value="true"/> + <conditional name="bed_style"> + <param name="arrowhead_included" value="true"/> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -1373,11 +1764,15 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 10--> <test> <param name="region" value="X:3340000-3380000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="top" /> + </conditional> + </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="gene_track_option" /> @@ -1419,17 +1814,21 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 11--> <test> <param name="region" value="chrX:3250000-3400000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="top" /> + </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)" /> - <param name="colormap" value="RdYlBu_r" /> + <!--<param name="colormap" value="RdYlBu_r" />--> <param name="depth" value="100000" /> <param name="transform" value="log1p" /> <param name="show_masked_bins" value="true" /> @@ -1448,10 +1847,12 @@ <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> <param name="title" value="TAD separation score (Ramirez et al.)" /> <param name="height_bedgraph" value="10" /> - <param name="type_lines" value="lines" /> - <param name="pos_score_in_bin" value="block" /> - <param name="plot_horizontal_lines" value="true" /> - <param name="show_data" value="true" /> + <conditional name="type"> + <param name="type_selector" value="lines" /> + <param name="pos_score_in_bin" value="block" /> + <param name="plot_horizontal_lines" value="true" /> + <param name="show_data" value="true" /> + </conditional> </conditional> </repeat> <repeat name="tracks"> @@ -1460,19 +1861,25 @@ <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> <param name="title" value="TAD separation score (Ramirez et al.)" /> <param name="height_bedgraph" value="10" /> - <param name="type_lines" value="lines" /> - <param name="pos_score_in_bin" value="center" /> - <param name="plot_horizontal_lines" value="false" /> + <conditional name="type"> + <param name="type_selector" value="lines" /> + <param name="pos_score_in_bin" value="center" /> + <param name="plot_horizontal_lines" value="false" /> + </conditional> </conditional> </repeat> <param name="image_file_format" value="png" /> <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 12--> <test> <param name="region" value="chrX:3000000-3300000"/> - <conditional name="x_axis"> - <param name="x_axis_select" value="true" /> - </conditional> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="top" /> + </conditional> + </repeat> <repeat name="tracks"> <conditional name="track_file_style_conditional"> <param name="track_file_style_selector" value="hic_matrix_option" /> @@ -1514,6 +1921,156 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 13--> + <test> + <param name="region" value="chrX:3000000-3300000"/> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="link_track_option" /> + <param name="track_input_link" value="test.arcs" ftype="bed" /> + <param name="title" value="default" /> + <conditional name="color_link"> + <param name="color_link_select" value="manually" /> + <param name="color" value="#000000" /> + </conditional> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="link_track_option" /> + <param name="track_input_link" value="test.arcs" ftype="bed" /> + <param name="title" value="ylim 20kb" /> + <conditional name="color_link"> + <param name="color_link_select" value="manually" /> + <param name="color" value="#000000" /> + </conditional> + <param name="ylim" value="20000" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="link_track_option" /> + <param name="track_input_link" value="test.arcs" ftype="bed" /> + <param name="title" value="compacted" /> + <conditional name="color_link"> + <param name="color_link_select" value="manually" /> + <param name="color" value="#000000" /> + </conditional> + <param name="compact_arcs_level" value="1" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="link_track_option" /> + <param name="track_input_link" value="test.arcs" ftype="bed" /> + <param name="title" value="highly compacted" /> + <conditional name="color_link"> + <param name="color_link_select" value="manually" /> + <param name="color" value="#000000" /> + </conditional> + <param name="compact_arcs_level" value="2" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="35000" /> + </test> + <!--test 14--> + <test> + <param name="region" value="chrX:3000000-3300000"/> + <section name="global_args"> + <param name="title" value="Scale bar"/> + <param name="trackLabelFraction" value="0.5"/> + <param name="trackLabelHAlign" value="center"/> + </section> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="spacer_option" /> + <param name="spacer_height" value="1.0" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="scale_bar_option" /> + <param name="title" value="default" /> + <param name="spacer_height" value="1"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="scale_bar_option" /> + <param name="title" value="scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5" /> + <param name="color" value="red"/> + <param name="alpha" value="0.5"/> + <param name="line_width" value="2"/> + <param name="x_center" value="3200000"/> + <param name="size" value="100002"/> + <param name="sb_where" value="right"/> + <param name="fontsize" value="8"/> + <param name="spacer_height" value="4"/> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="35000" /> + </test> + <!--test 15--> + <test> + <param name="region" value="chrX:3300000-3500000"/> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="bottom" /> + </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="flybase" /> + <param name="height_bed" value="10" /> + </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="UCSC" /> + <param name="height_bed" value="10" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="UCSC"/> + <section name="bed_advanced"> + <param name="arrow_interval" value="10"/> + </section> + </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="dm3_genes.bed.gz" ftype="bed" /> + <param name="title" value="tssarrow" /> + <param name="height_bed" value="10" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="tssarrow"/> + </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="dm3_genes.bed.gz" ftype="bed" /> + <param name="title" value="tssarrow 5kb" /> + <param name="height_bed" value="10" /> + <conditional name="bed_style"> + <param name="bed_style_select" value="tssarrow"/> + <section name="bed_advanced"> + <param name="arrow_length" value="5000"/> + </section> + </conditional> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" /> + </test> </tests> <help><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test13.ini Fri Apr 17 11:57:44 2020 -0400 @@ -0,0 +1,49 @@ +[links_1] +file = test.arcs +title = default +height = 1.5 +color = #000000 +alpha = 1.0 +line_width = 0.5 +line_style = solid +links_type = arcs +compact_arcs_level = 0 +overlay_previous = no +file_type = links +[links_2] +file = test.arcs +title = ylim 20kb +height = 1.5 +color = #000000 +alpha = 1.0 +line_width = 0.5 +line_style = solid +links_type = arcs +compact_arcs_level = 0 +ylim = 20000.0 +overlay_previous = no +file_type = links +[links_3] +file = test.arcs +title = compacted +height = 1.5 +color = #000000 +alpha = 1.0 +line_width = 0.5 +line_style = solid +links_type = arcs +compact_arcs_level = 1 +overlay_previous = no +file_type = links +[links_4] +file = test.arcs +title = highly compacted +height = 1.5 +color = #000000 +alpha = 1.0 +line_width = 0.5 +line_style = solid +links_type = arcs +compact_arcs_level = 2 +overlay_previous = no +file_type = links
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test14.ini Fri Apr 17 11:57:44 2020 -0400 @@ -0,0 +1,23 @@ +[spacer] +height = 1.0 +[scale_bar] +title = default +color = #000000 +alpha = 1.0 +line_width = 0.5 +where = left +file_type = scalebar +[spacer] +height = 1.0 +[scale_bar] +title = scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5 +color = red +alpha = 0.5 +line_width = 2.0 +x_center = 3200000 +size = 100002 +where = right +fontsize = 8.0 +file_type = scalebar +[spacer] +height = 4.0 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test15.ini Fri Apr 17 11:57:44 2020 -0400 @@ -0,0 +1,67 @@ +[x-axis] +where = bottom +[genes_1_0] +file = dm3_genes.bed.gz +title = flybase +color = #000000 +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = grey +arrowhead_included = false +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +overlay_previous = no +[genes_2_0] +file = dm3_genes.bed.gz +title = UCSC +color = #000000 +border_color = #000000 +style = UCSC +arrow_interval = 10 +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +overlay_previous = no +[genes_3_0] +file = dm3_genes.bed.gz +title = tssarrow +color = #000000 +border_color = #000000 +style = tssarrow +height_utr = 1.0 +color_utr = grey +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +overlay_previous = no +[genes_4_0] +file = dm3_genes.bed.gz +title = tssarrow 5kb +color = #000000 +border_color = #000000 +style = tssarrow +height_utr = 1.0 +color_utr = grey +arrow_length = 5000 +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +overlay_previous = no \ No newline at end of file
--- a/test-data/test3.ini Tue Feb 11 10:20:24 2020 -0500 +++ b/test-data/test3.ini Fri Apr 17 11:57:44 2020 -0400 @@ -149,7 +149,7 @@ overlay_previous = no [genes_12_0] file = test-data/domains.bed -title = domains.bed using the 9th field for colors interleaved +title = domains.bed using the 9th field for colors interleaved border=red color = bed_rgb border_color = red style = flybase @@ -164,4 +164,40 @@ max_labels = 60 line_width = 0.5 arrowhead_included = false +overlay_previous = no +[genes_13_0] +file = test-data/domains.bed +title = domains.bed using the 9th field for colors interleaved border=bed_rgb +color = bed_rgb +border_color = bed_rgb +style = flybase +height_utr = 1.0 +color_utr = grey +display = interleaved +height = 2.0 +labels = false +file_type = bed +fontsize = 10 +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[genes_14_0] +file = test-data/domains.bed +title = domains.bed using the 9th field for colors interleaved border=none +color = bed_rgb +border_color = none +style = flybase +height_utr = 1.0 +color_utr = grey +display = interleaved +height = 2.0 +labels = false +file_type = bed +fontsize = 10 +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false overlay_previous = no \ No newline at end of file
--- a/test-data/test6.ini Tue Feb 11 10:20:24 2020 -0500 +++ b/test-data/test6.ini Fri Apr 17 11:57:44 2020 -0400 @@ -10,6 +10,17 @@ overlay_previous = no [narrow_peak_1_0] file = test-data/test2.narrowPeak +title = box line_width = 2 +color = #9bbb59 +type = box +use_summit = true +height = 4.0 +show_labels = true +line_width = 2 +file_type = narrow_peak +overlay_previous = no +[narrow_peak_2_0] +file = test-data/test2.narrowPeak title = peak width 3 color = #c0504d type = peak @@ -23,7 +34,7 @@ overlay_previous = no [spacer] height = 0.5 -[narrow_peak_2_0] +[narrow_peak_3_0] file = test-data/test2.narrowPeak title = peak no data range color = #000000
--- a/test-data/test7.ini Tue Feb 11 10:20:24 2020 -0500 +++ b/test-data/test7.ini Fri Apr 17 11:57:44 2020 -0400 @@ -35,4 +35,74 @@ max_labels = 60 line_width = 0.5 arrowhead_included = false +overlay_previous = no +[genes_2_0] +file = test-data/dm3_genes_withrgbandscore.bed.gz +title = genes with scores +color = cool_r +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = grey +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[genes_3_0] +file = test-data/dm3_genes_withrgbandscore.bed.gz +title = genes with utr as bed_rgb +color = black +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = bed_rgb +display = stacked +height = 10.0 +labels = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[genes_3_0] +file = test-data/dm3_genes_withrgbandscore.bed.gz +title = genes with coding as bed_rgb - labels_in_margin +color = bed_rgb +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = grey +display = stacked +height = 10.0 +labels = true +labels_in_margin = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false +overlay_previous = no +[genes_4_0] +file = test-data/dm3_genes_withrgbandscore.bed.gz +title = genes bed_rgb like - all_labels_inside +color = bed_rgb +border_color = #000000 +style = flybase +height_utr = 1.0 +color_utr = bed_rgb +display = stacked +height = 10.0 +labels = true +all_labels_inside = true +file_type = bed +global_max_row = false +max_labels = 60 +line_width = 0.5 +arrowhead_included = false overlay_previous = no \ No newline at end of file
--- a/test-data/testpyGT.sh Tue Feb 11 10:20:24 2020 -0500 +++ b/test-data/testpyGT.sh Fri Apr 17 11:57:44 2020 -0400 @@ -11,5 +11,8 @@ pgt --tracks test-data/test10.ini --region X:3340000-3380000 -o test-data/test_middle_triangle.png pgt --tracks test-data/test11.ini --region chrX:3250000-3400000 -o test-data/test_TADs_bdgm.png pgt --tracks test-data/test12.ini --region chrX:3000000-3300000 -o test-data/test_link.png +pgt --tracks test-data/test13.ini --region chrX:3000000-3300000 -o test-data/test_link2.png +pgt --tracks test-data/test14.ini --region chrX:3000000-3300000 --title "Scale bar" --trackLabelFraction 0.5 --trackLabelHAlign center -o test-data/test_scale_bar.png +pgt --tracks test-data/test15.ini --region chrX:3300000-3500000 -o test-data/test_tssarrow.png conda_env_deactivate