| Previous changeset 1:0ea86f6bf2a1 (2018-07-02) Next changeset 3:feab9265552d (2019-08-26) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" |
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modified:
macros.xml pyGenomeTracks.xml test-data/bigwig_multiple.png test-data/dm3_genes.bed6.gz test-data/master_TADs_plot.png |
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added:
test-data/bigwig_multiple_before.png test-data/dm3_subset_BDGP5.78.gtf.gz test-data/dm3_subset_BDGP5.78_asbed4.bed.gz test-data/master_TADs_BW_plot.png test-data/master_TADs_plot_before.png test-data/test_alpha.png test-data/test_gtf_bed4.png test-data/test_with_neg_values.bg.gz |
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| diff -r 0ea86f6bf2a1 -r c171f2b7d76e macros.xml --- a/macros.xml Mon Jul 02 19:32:13 2018 -0400 +++ b/macros.xml Fri Aug 23 07:24:20 2019 -0400 |
| [ |
| b'@@ -1,12 +1,13 @@\n <macros>\n <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n- <token name="@WRAPPER_VERSION@">2.0</token>\n+ <token name="@WRAPPER_VERSION@">3.1</token>\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement>\n+ <!--<requirement type="package" version="3.7">python</requirement>-->\n <yield />\n </requirements>\n- <version_command>@BINARY@ --version</version_command>\n+ <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command>\n </xml>\n \n <xml name="citations">\n@@ -188,6 +189,9 @@\n <xml name="track_input_bed_macro">\n <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple=\'True\'/>\n </xml>\n+ <xml name="track_input_bed_gtf_macro">\n+ <param name="track_input_bed" type="data" format="bed,gtf" label="Track file bed or gtf format" multiple=\'True\'/>\n+ </xml>\n <xml name="track_input_bed_single_macro">\n <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/>\n </xml>\n@@ -207,4 +211,219 @@\n <param name="spacer_height" type="float" value="" optional="True"\n label="Include spacer at the end of the track" help="Height of the spacer." />\n </xml>\n+ <xml name="inverted_macro">\n+ <param name="invert_orientation" type="boolean" truevalue="yes" falsevalue="no" checked="false"\n+ label="Invert the track" />\n+ </xml>\n+ <xml name="color_bed_macro">\n+ <conditional name="color_bed">\n+ <param name="color_bed_select" type="select" label="Use color:">\n+ <option value="manually" selected="True">manually</option>\n+ <option value="bed_rgb">From the 9th field</option>\n+ <option value="colormap">From the 5th field (score)</option>\n+ </param>\n+ <when value="manually">\n+ <param name="color" type="color" value="#000000" label="Color of track" optional="True" />\n+ </when>\n+ <when value="bed_rgb" />\n+ <when value="colormap">\n+ <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">\n+ <option value="RdYlBu">RdYlBu</option>\n+ <option value="Accent">Accent</option>\n+ <option value="Spectral">Spectral</option>\n+ <option value="Set1">Set1</option>\n+ <option value="Set2">Set2</option>\n+ <option value="Set3">Set3</option>\n+ <option value="Dark2">Dark2</option>\n+ <option value="Reds">Reds</option>\n+ <option value="Oranges">Oranges</option>\n+ <option value="Greens">Greens</option>\n+ <option value="Blues">Blues</option>\n+ <option value="Greys">Greys</option>\n+ <option value="Purples">Purples</option>\n+ <option value="Paired">Paired</option>\n+ <option value="Pastel1">Pastel1</option>\n+ <option value="Pastel2">Pastel2</option>\n+ <option value="spring">spring</option>\n+ <option value="summer">summer</option>\n+ <option value="autumn">autumn</option>\n+ <option value="winter">winter</option>\n+ <option value="hot">hot</option>\n+ <option value="coolwarm">coolwarm</option>\n+ <option value="cool">cool</option>\n+ <option value="seismic">seismic</option>\n+ <option value="terrain">terrain</option>\n+ <option value="ocean">ocean</option>\n+ <option value="rainbow">rainbow</option>\n+ <option value="bone">bone</option>\n+ <opt'..b' <option value="gist_ncar_r">gist_ncar reversed</option>\n+ <option value="gist_rainbow_r">gist_rainbow reversed</option>\n+ <option value="gist_heat_r">gist_heat reversed</option>\n+ <option value="gnuplot_r">gnuplot reversed</option>\n+ <option value="gnuplot2_r">gnuplot2 reversed</option>\n+ <option value="CMRmap_r">CMRmap reversed</option>\n+ <option value="bwr_r">bwr reversed</option>\n+ <option value="hsv_r">hsv reversed</option>\n+ <option value="brg_r">brg reversed</option>\n+ <option value="jet_r">jet reversed</option>\n+ <option value="afmhot_r">afmhot reversed</option>\n+ </param>\n+ </when>\n+ </conditional>\n+ <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />\n+ </xml>\n+ <xml name="color_coverage_macro">\n+ <param name="color" type="color" value="#000000" label="Color of track" optional="True" />\n+ <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"/>\n+ <conditional name="color_negative">\n+ <param name="color_negative_select" type="select" label="Use a different color for negative values">\n+ <option value="no" selected="True">No</option>\n+ <option value="yes">Yes</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <param name="color" type="color" value="#000000" label="Color of negative values" optional="True" />\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="overlay_macro">\n+ <param name="overlay_select" type="select" label="Overlay this track with the previous one:">\n+ <option value="no" selected="True">No</option>\n+ <option value="yes">Yes</option>\n+ <option value="share-y">Yes and keep same y axis</option>\n+ </param>\n+ </xml>\n+ <xml name="type_coverage_macro">\n+ <conditional name="type_conditional">\n+ <param name="type_selector" type="select" label="Choose style of the plot.">\n+ <option value="fill_option">fill</option>\n+ <option value="line_option">line</option>\n+ <option value="point_option">point</option>\n+ </param>\n+ <when value="line_option">\n+ <param name="width_line" type="float" value="0.5" optional="True" label="Width"/>\n+ </when>\n+ <when value="point_option">\n+ <param name="width_point" type="float" value="0.5" optional="True" label="Width"/>\n+ </when>\n+ <when value="fill_option" />\n+ </conditional>\n+ </xml>\n+ <xml name="minmax_macro">\n+ <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>\n+ <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>\n+ </xml>\n+ <xml name="reading_bw_macro">\n+ <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False">\n+ <param name="summary" type="select" label="Summary method">\n+ <option value="mean" selected="True">mean=mean value</option>\n+ <option value="min">min=minimum value</option>\n+ <option value="max">max=maximum value</option>\n+ <option value="coverage">coverage=number of covered bases</option>\n+ <option value="std">std=standard deviation</option>\n+ </param>\n+ <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />\n+ <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false"\n+ label="NAN\'s to zeros" />\n+ </section>\n+ </xml>\n </macros>\n' |
| b |
| diff -r 0ea86f6bf2a1 -r c171f2b7d76e pyGenomeTracks.xml --- a/pyGenomeTracks.xml Mon Jul 02 19:32:13 2018 -0400 +++ b/pyGenomeTracks.xml Fri Aug 23 07:24:20 2019 -0400 |
| [ |
| b'@@ -7,6 +7,21 @@\n <expand macro="requirements" />\n <command detect_errors="exit_code">\n <![CDATA[\n+ #for $counter, $track in enumerate($tracks):\n+ #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":\n+ #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):\n+ #set ext = $data_matrix.extension\n+ ln -s $data_matrix ${counter}_${counter_matrix}.$ext &&\n+ #end for\n+ #end if\n+ #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":\n+ #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):\n+ #set ext = $data_bed.extension\n+ ln -s $data_bed ${counter}_${counter_bed}.$ext &&\n+ #end for\n+ #end if\n+ #end for\n+\n \n sed \'/^$/d\' \'$tracks_config\' &&\n @BINARY@\n@@ -35,8 +50,9 @@\n #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":\n \n #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):\n-[hic_section_$counter]\n-file = $data_matrix\n+[hic_section_${counter}_${counter_matrix}]\n+#set ext = $data_matrix.extension\n+file = ${counter}_${counter_matrix}.$ext\n file_type = hic_matrix\n #if $track.track_file_style_conditional.title:\n title = $track.track_file_style_conditional.title\n@@ -55,29 +71,40 @@\n #if $track.track_file_style_conditional.max_value:\n max_value = $track.track_file_style_conditional.max_value\n #end if\n+#if $track.track_file_style_conditional.transform != "":\n transform = $track.track_file_style_conditional.transform\n+#end if\n+#if $track.track_file_style_conditional.height_matrix != "":\n height = $track.track_file_style_conditional.height_matrix\n-\n-#if $track.track_file_style_conditional.boundaries_file is not None:\n-#set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]\n-boundaries_file = $boundary_file\n #end if\n \n-#if $track.track_file_style_conditional.x_labels:\n-x labels = $track.track_file_style_conditional.x_labels\n-#end if\n-#if $track.track_file_style_conditional.type:\n-type = $track.track_file_style_conditional.type\n-#end if\n #if $track.track_file_style_conditional.show_masked_bins:\n show_masked_bins = $track.track_file_style_conditional.show_masked_bins\n #end if\n+#if $track.track_file_style_conditional.invert_orientation:\n+orientation = inverted\n+#end if\n #if $track.track_file_style_conditional.scale_factor:\n scale factor = $track.track_file_style_conditional.scale_factor\n #end if\n \n+#if str($track.track_file_style_conditional.boundaries_file) != "None":\n+#if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix:\n+#set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]\n+#else:\n+#set boundary_file = $track.track_file_style_conditional.boundaries_file[0]\n+#end if\n+[tads_${counter}_${counter_matrix}]\n+file = $boundary_file\n+file_type = domains\n+border color = black\n+color = none\n+overlay previous = share-y\n+#end if\n+\n+\n+#if $track.track_file_style_conditional.spacer_height != "":\n [spacer]\n-#if $track.track_file_style_conditional.spacer_height:\n height = $track.track_file_style_conditional.spacer_height\n #end if\n #end for\n@@ -90,7 +117,7 @@\n \n #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:\n [tad_score_$counter]\n-file = $data_bedgraph \n+file = $data_bedgraph\n #if $track.track_file_style_conditional.title:\n title = $track.track_file_style_conditional.title\n #else:\n@@ -102,22 +129,21 @@\n #if $track.track_file_style_conditional.height_tad:\n height = $track.track_file_style_conditional.height_tad\n #end if\n-#if $track.track_file_style_conditional.type_lines:\n-type = $track.track_file_style_conditional.type_lines\n-#end if\n #if $track.track_file_st'..b'f0000" />\n+ <param name="alpha" value="0.5" />\n+ <param name="summary" value="max" />\n+ <param name="number_of_bins" value="300"/>\n+ <param name="overlay_select" value="share-y"/>\n+ </conditional>\n+ </repeat>\n+ <param name="image_file_format" value="png" />\n+ <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" />\n+ </test>\n+ <test>\n+ <param name="region" value="X:3000000-3300000"/>\n+ <conditional name="x_axis">\n+ <param name="x_axis_select" value="yes" />\n+ </conditional>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="gene_track_option" />\n+ <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />\n+ <param name="title" value="test" />\n+ <param name="height_bed" value="10" />\n+ <param name="color" value="#000000" />\n+ <param name="flybase" value="false" />\n+ <param name="spacer_height" value="1"/>\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="gene_track_option" />\n+ <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />\n+ <param name="title" value="test" />\n+ <param name="height_bed" value="10" />\n+ <param name="color" value="#000000" />\n+ <param name="flybase" value="false" />\n+ <param name="spacer_height" value="1"/>\n+ </conditional>\n+ </repeat>\n+ <param name="image_file_format" value="png" />\n+ <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" />\n+ </test>\n </tests>\n <help><
