# HG changeset patch # User iuc # Date 1595316768 14400 # Node ID 4ac4e7083b7ef971a275b0391ca8e4604eb7f21f # Parent 326a3db8d9d1e5bc4eaccdd71e7fadee7d8f59da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" diff -r 326a3db8d9d1 -r 4ac4e7083b7e macros.xml --- a/macros.xml Fri Apr 17 11:57:44 2020 -0400 +++ b/macros.xml Tue Jul 21 03:32:48 2020 -0400 @@ -1,6 +1,6 @@ \${GALAXY_SLOTS:-4} - 3.3 + 3.5 pygenometracks @@ -114,6 +114,43 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 326a3db8d9d1 -r 4ac4e7083b7e pyGenomeTracks.xml --- a/pyGenomeTracks.xml Fri Apr 17 11:57:44 2020 -0400 +++ b/pyGenomeTracks.xml Tue Jul 21 03:32:48 2020 -0400 @@ -7,7 +7,7 @@ @@ -144,7 +139,7 @@ #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): [genes_${counter}_${counter_bed}] #set ext = $data_bed.extension -file = ${counter}_${counter_bed}.$ext +file = $data_bed #if $ext == 'gtf': 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 @@ -196,7 +191,7 @@ 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 +file_type = $ext #if $track.track_file_style_conditional.fontsize: fontsize = $track.track_file_style_conditional.fontsize #end if @@ -245,6 +240,7 @@ #if $track.track_file_style_conditional.ylim != "": ylim = $track.track_file_style_conditional.ylim #end if +use_middle = $track.track_file_style_conditional.use_middle #if $track.track_file_style_conditional.invert_orientation: orientation = inverted #end if @@ -330,6 +326,7 @@ max_value = $track.track_file_style_conditional.max_value #end if show_data_range = $track.track_file_style_conditional.show_data +grid = $track.track_file_style_conditional.grid nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros use_middle = $track.track_file_style_conditional.use_middle #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) @@ -345,6 +342,25 @@ #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': type = points:$track.track_file_style_conditional.type_conditional.width_point #end if + #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no': +transform = $track.track_file_style_conditional.logScale_conditional.transform_selector +y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values + #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p': +log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount + #end if + #end if + #end if + #if $track.track_file_style_conditional.reading_bdg_as_bw.summary_method != 'no': +summary_method = $track.track_file_style_conditional.reading_bdg_as_bw.summary_method + #if $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins: +number_of_bins = $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins + #end if + #end if + #if $track.track_file_style_conditional.op.operation != 'file': +operation = $track.track_file_style_conditional.op.operation + #if 'second_file' in str($track.track_file_style_conditional.op.operation): +second_file = $track.track_file_style_conditional.op.second_file + #end if #end if #if $track.track_file_style_conditional.invert_orientation: orientation = inverted @@ -382,7 +398,7 @@ max_value = $track.track_file_style_conditional.max_value #end if height = $track.track_file_style_conditional.height_bigwig -summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary +summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary_method nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins: number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins @@ -394,7 +410,21 @@ #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': type = points:$track.track_file_style_conditional.type_conditional.width_point #end if + #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no': +transform = $track.track_file_style_conditional.logScale_conditional.transform_selector +y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values + #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p': +log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount + #end if + #end if + #if $track.track_file_style_conditional.op.operation != 'file': +operation = $track.track_file_style_conditional.op.operation + #if 'second_file' in $track.track_file_style_conditional.op.operation: +second_file = $track.track_file_style_conditional.op.second_file + #end if + #end if show_data_range = $track.track_file_style_conditional.show_data +grid = $track.track_file_style_conditional.grid file_type = bigwig #if $track.track_file_style_conditional.invert_orientation: orientation = inverted @@ -451,6 +481,7 @@ #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": [vlines_$counter] file = $track.track_file_style_conditional.track_input_bed_single +line_width = $track.track_file_style_conditional.line_width type = vlines #end if @@ -562,6 +593,8 @@ + highly compacted (the height is the same for all distances) + + + + @@ -792,11 +829,29 @@ +
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+ @@ -811,7 +866,7 @@
- + @@ -823,7 +878,14 @@ label="NAN's to zeros" />
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