Mercurial > repos > iuc > pygenometracks
diff pyGenomeTracks.xml @ 8:4ac4e7083b7e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
| author | iuc |
|---|---|
| date | Tue, 21 Jul 2020 03:32:48 -0400 |
| parents | 326a3db8d9d1 |
| children | 2824d77cd8f8 |
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--- 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 @@ <expand macro="requirements" /> <command detect_errors="exit_code"> <![CDATA[ - ## First symlink data of hic or bed/gtf to have the good extension + ## First symlink data of hic to have the good extension #for $counter, $track in enumerate($tracks): #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): @@ -15,12 +15,6 @@ ln -s $data_matrix ${counter}_${counter_matrix}.$ext && #end for #end if - #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": - #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): - #set ext = $data_bed.extension - ln -s $data_bed ${counter}_${counter_bed}.$ext && - #end for - #end if #end for @@ -38,6 +32,7 @@ --trackLabelFraction $global_args.trackLabelFraction --trackLabelHAlign $global_args.trackLabelHAlign --outFileName plot.$image_file_format + $global_args.decreasingXAxis && mv plot.$image_file_format plot ]]> </command> @@ -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 @@ <option value="right">right</option> <option value="center">center</option> </param> + <param argument="--decreasingXAxis" type="boolean" truevalue="--decreasingXAxis" falsevalue="" checked="false" + label="Use a decreasing x axis" help="By default, the x-axis is increasing. Use this option if you want to see all tracks with a decreasing x-axis."/> </section> <!--Info to build the config file--> <repeat name="tracks" min="1" title="Include tracks in your plot" @@ -746,6 +779,10 @@ <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="use_middle" type="select" label="Coordinates to use" help="Not useful with loops"> + <option value="false" selected="True">Extremities (start of first and end of second)</option> + <option value="true">Center (mean of start and end for each)</option> + </param> <param name="height" type="float" value="1.5" optional="True" label="height"/> <expand macro="minmax_macro" /> <expand macro="overlay_macro" /> @@ -792,11 +829,29 @@ <expand macro="minmax_macro" /> <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> <expand macro="type_coverage_macro" /> + <section name="reading_bdg_as_bw" title="Configure bigwig parameters" expanded="False"> + <param name="summary_method" type="select" label="Summary method"> + <option value="no" selected="True">no=no summary method (keep all values)</option> + <option value="mean">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" /> + </section> + <expand macro="logScale_coverage_macro" /> + <section name ="op" title="Compute an operation on the file" expanded="False"> + <param name="operation" type="text" label="operation to compute on the file(s)" value="file" + help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/> + <param name="second_file" type="data" format="bedgraph" label="second_file (bedgraph format)" multiple="False" optional="True"/> + </section> <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false" label="NAN's to zeros" /> <param name="use_middle" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use middle: Instead of using start and end, use the middle of intervals (useful for 4C-seq tracks)." /> <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" /> + <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" /> <expand macro="inverted_macro" /> <expand macro="overlay_macro" /> <expand macro="spacer_macro" /> @@ -811,7 +866,7 @@ <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False"> - <param name="summary" type="select" label="Summary method"> + <param name="summary_method" 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> @@ -823,7 +878,14 @@ label="NAN's to zeros" /> </section> <expand macro="type_coverage_macro" /> + <expand macro="logScale_coverage_macro" /> + <section name ="op" title="Compute an operation on the file" expanded="False"> + <param name="operation" type="text" label="operation to compute on the file(s)" value="file" + help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/> + <param name="second_file" type="data" format="bigwig" label="second_file (bedgraph format)" multiple="False" optional="True"/> + </section> <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> + <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" /> <expand macro="inverted_macro" /> <expand macro="overlay_macro" /> <expand macro="spacer_macro" /> @@ -868,6 +930,7 @@ </when> <when value="vlines_track_option"> <expand macro="track_input_bed_single_macro" /> + <param name="line_width" type="float" value="0.5" label="width of lines"/> </when> <when value="hlines_track_option"> <expand macro="plot_title" /> @@ -1280,7 +1343,7 @@ <param name="width_point" value="5" /> </conditional> <section name="reading_bw_conditional"> - <param name="summary" value="max"/> + <param name="summary_method" value="max"/> <param name="number_of_bins" value="100"/> </section> </conditional> @@ -1295,7 +1358,7 @@ <param name="type_selector" value="line_option" /> </conditional> <section name="reading_bw_conditional"> - <param name="summary" value="min"/> + <param name="summary_method" value="min"/> </section> <param name="overlay_select" value="share-y" /> </conditional> @@ -1310,7 +1373,7 @@ <param name="type_selector" value="line_option" /> </conditional> <section name="reading_bw_conditional"> - <param name="summary" value="min"/> + <param name="summary_method" value="min"/> <param name="number_of_bins" value="30000"/> </section> <param name="overlay_select" value="share-y" /> @@ -1430,7 +1493,7 @@ <param name="title" value="" /> <param name="color" value="#ff0000" /> <param name="alpha" value="0.5" /> - <param name="summary" value="max" /> + <param name="summary_method" value="max" /> <section name="reading_bw_conditional"> <param name="number_of_bins" value="300"/> </section> @@ -2071,6 +2134,481 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <!--test 16--> + <test> + <param name="region" value="X:2700000-3100000"/> + <section name="global_args"> + <param name="decreasingXAxis" value="true"/> + </section> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bigwig_track_option" /> + <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> + <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" /> + <param name="height_bigwig" value="7" /> + <param name="color" value="#00b0f0" /> + <section name="reading_bw_conditional"> + <param name="number_of_bins" value="2000"/> + </section> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bigwig_track_option" /> + <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> + <param name="title" value="" /> + <param name="color" value="#ff0000" /> + <param name="alpha" value="0.5" /> + <param name="summary_method" value="max" /> + <section name="reading_bw_conditional"> + <param name="number_of_bins" value="300"/> + </section> + <param name="overlay_select" value="share-y"/> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="xaxis_option" /> + <param name="xaxis_where" value="bottom" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="35000" /> + </test> + <!--test 17--> + <test> + <param name="region" value="chr2:73,800,000-75,744,000"/> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = blue transform = no" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="blue" /> + <param name="show_data" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = blue transform = log" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="blue" /> + <conditional name="logScale_conditional"> + <param name="transform_selector" value="log"/> + </conditional> + <param name="show_data" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = red transform = log min_value = 1" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="red" /> + <conditional name="logScale_conditional"> + <param name="transform_selector" value="log"/> + </conditional> + <param name="min_value" value="1" /> + <param name="show_data" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="green" /> + <conditional name="logScale_conditional"> + <param name="transform_selector" value="log"/> + <param name="log_pseudocount" value="2"/> + </conditional> + <param name="min_value" value="0" /> + <param name="show_data" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="green" /> + <section name="op"> + <param name="operation" value="log(2+file)" /> + </section> + <param name="min_value" value="0.7" /> + <param name="show_data" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="black" /> + <conditional name="logScale_conditional"> + <param name="transform_selector" value="log2"/> + <param name="log_pseudocount" value="1"/> + </conditional> + <param name="min_value" value="0" /> + <param name="show_data" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="black" /> + <section name="op"> + <param name="operation" value="log2(1+file)" /> + </section> + <param name="min_value" value="0" /> + <param name="show_data" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="black" /> + <conditional name="logScale_conditional"> + <param name="transform_selector" value="log2"/> + <param name="log_pseudocount" value="1"/> + <param name="y_axis_values" value="original"/> + </conditional> + <param name="min_value" value="0" /> + <param name="show_data" 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_log.png" ftype="png" compare="sim_size" delta="35000" /> + </test> + <!--test 18--> + <test> + <param name="region" value="chrX:2700000-3100000"/> + <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="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> + <param name="title" value="file summary_method = mean number_of_bins=20" /> + <param name="height_bedgraph" value="4" /> + <param name="color" value="blue" /> + <param name="show_data" value="true" /> + <section name="reading_bdg_as_bw" > + <param name="summary_method" value="mean" /> + <param name="number_of_bins" value="20" /> + </section> + <param name="min_value" value="0" /> + <param name="max_value" value="30" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" /> + <param name="title" value="second_file summary_method = mean" /> + <param name="height_bedgraph" value="4" /> + <param name="color" value="red" /> + <param name="show_data" value="true" /> + <section name="reading_bdg_as_bw" > + <param name="summary_method" value="mean" /> + </section> + <param name="min_value" value="0" /> + <param name="max_value" value="30" /> + <param name="spacer_height" value="0.5" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> + <param name="title" value="operation = log1p(file) (no summary_method)" /> + <param name="height_bedgraph" value="4" /> + <param name="color" value="blue" /> + <param name="show_data" value="true" /> + <section name="op"> + <param name="operation" value="log1p(file)" /> + </section> + <param name="spacer_height" value="0.5" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> + <param name="title" value="operation = file - second_file" /> + <param name="height_bedgraph" value="8" /> + <param name="color" value="blue" /> + <param name="show_data" value="true" /> + <conditional name="color_negative"> + <param name="color_negative_select" value="true" /> + <param name="color" value="red" /> + </conditional> + <section name="op"> + <param name="operation" value="file - second_file" /> + <param name="second_file" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" /> + </section> + <param name="min_value" value="-30" /> + <param name="max_value" value="30" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="35000" /> + </test> + <!--test 19--> + <test> + <param name="region" value="chr2:73,800,000-75,744,000"/> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = blue transform = no" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="blue" /> + <param name="show_data" value="true" /> + <param name="grid" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = blue transform = log" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="blue" /> + <conditional name="logScale_conditional"> + <param name="transform_selector" value="log"/> + </conditional> + <param name="show_data" value="true" /> + <param name="grid" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = red transform = log min_value = 1" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="red" /> + <conditional name="logScale_conditional"> + <param name="transform_selector" value="log"/> + </conditional> + <param name="min_value" value="1" /> + <param name="show_data" value="true" /> + <param name="grid" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="green" /> + <conditional name="logScale_conditional"> + <param name="transform_selector" value="log"/> + <param name="log_pseudocount" value="2"/> + </conditional> + <param name="min_value" value="0" /> + <param name="show_data" value="true" /> + <param name="grid" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="green" /> + <section name="op"> + <param name="operation" value="log(2+file)" /> + </section> + <param name="min_value" value="0.7" /> + <param name="show_data" value="true" /> + <param name="grid" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="black" /> + <conditional name="logScale_conditional"> + <param name="transform_selector" value="log2"/> + <param name="log_pseudocount" value="1"/> + </conditional> + <param name="min_value" value="0" /> + <param name="show_data" value="true" /> + <param name="grid" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="black" /> + <section name="op"> + <param name="operation" value="log2(1+file)" /> + </section> + <param name="min_value" value="0" /> + <param name="show_data" value="true" /> + <param name="grid" value="true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="bedgraph_track_option" /> + <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" /> + <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" /> + <param name="height_bedgraph" value="5" /> + <param name="color" value="black" /> + <conditional name="logScale_conditional"> + <param name="transform_selector" value="log2"/> + <param name="log_pseudocount" value="1"/> + <param name="y_axis_values" value="original"/> + </conditional> + <param name="min_value" value="0" /> + <param name="show_data" value="true" /> + <param name="grid" 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_log_grid.png" ftype="png" compare="sim_size" delta="35000" /> + </test> + <!--test 20--> + <test> + <param name="region" value="chrX:3000000-3300000"/> + <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="spacer_option" /> + <param name="spacer_height" value="0.05" /> + </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="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" /> + <param name="depth" value="300000" /> + <param name="transform" value="log1p" /> + <param name="min_value" value="5" /> + <param name="show_masked_bins" value="false" /> + </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_wide.arcs" ftype="bed" /> + <conditional name="color_link"> + <param name="color" value="red" /> + </conditional> + <param name="line_width" value="5" /> + <param name="links_type" value="loops" /> + <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="link_track_option" /> + <param name="track_input_link" value="test_wide.arcs" ftype="bed" /> + <conditional name="color_link"> + <param name="color" value="RdYlGn" /> + </conditional> + <param name="line_width" value="3" /> + <param name="invert_orientation" value="true" /> + <param name="title" value="links line_width = 3 color RdYlGn" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="spacer_option" /> + <param name="spacer_height" value="1" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="hic_matrix_option" /> + <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> + <param name="title" value="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" /> + <param name="depth" value="300000" /> + <param name="transform" value="log1p" /> + <param name="min_value" value="5" /> + <param name="show_masked_bins" value="false" /> + </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_wide.arcs" ftype="bed" /> + <conditional name="color_link"> + <param name="color" value="red" /> + </conditional> + <param name="line_width" value="5" /> + <param name="links_type" value="loops" /> + <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="link_track_option" /> + <param name="track_input_link" value="test_wide.arcs" ftype="bed" /> + <conditional name="color_link"> + <param name="color" value="RdYlGn" /> + </conditional> + <param name="line_width" value="3" /> + <param name="invert_orientation" value="true" /> + <param name="use_middle" value="true" /> + <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" /> + </conditional> + </repeat> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="vlines_track_option" /> + <param name="track_input_bed_single" value="tad_classification.bed" ftype="bed" /> + <param name="line_width" value="3" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="35000" /> + </test> </tests> <help><![CDATA[