Mercurial > repos > iuc > pygenometracks
changeset 4:c237ba772225 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
| author | iuc |
|---|---|
| date | Thu, 19 Sep 2019 17:18:54 -0400 |
| parents | feab9265552d |
| children | eca03db4f612 |
| files | macros.xml pyGenomeTracks.xml test-data/bigwig_multiple.png test-data/bigwig_multiple_before.png test-data/master_TADs_BW_plot.png test-data/master_TADs_plot.png test-data/master_TADs_plot_before.png test-data/test2.narrowPeak test-data/test_alpha.png test-data/test_narrowPeak.png |
| diffstat | 10 files changed, 150 insertions(+), 14 deletions(-) [+] |
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--- a/macros.xml Mon Aug 26 06:20:55 2019 -0400 +++ b/macros.xml Thu Sep 19 17:18:54 2019 -0400 @@ -1,6 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">3.1</token> + <token name="@WRAPPER_VERSION@">3.1.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement> @@ -192,6 +192,9 @@ <xml name="track_input_bed_gtf_macro"> <param name="track_input_bed" type="data" format="bed,gtf" label="Track file bed or gtf format" multiple='True'/> </xml> + <xml name="track_input_narrow_peak_macro"> + <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file encodepeak or 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>
--- a/pyGenomeTracks.xml Mon Aug 26 06:20:55 2019 -0400 +++ b/pyGenomeTracks.xml Thu Sep 19 17:18:54 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.2"> +<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.1"> <description>plot genomic data tracks</description> <macros> <token name="@BINARY@">pyGenomeTracks</token> @@ -129,9 +129,7 @@ #if $track.track_file_style_conditional.height_tad: height = $track.track_file_style_conditional.height_tad #end if -#if $track.track_file_style_conditional.show_data: show data range = $track.track_file_style_conditional.show_data -#end if #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) #if $columns > 4: @@ -239,6 +237,51 @@ #end for #end if +#if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option": +#for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak): + +[narrow_peak_${counter}_${counter_narrow_peak}] +file = $data_narrow_peak +#if $track.track_file_style_conditional.title: +title = $track.track_file_style_conditional.title +#else: +title = $data_narrow_peak.name +#end if +color = $track.track_file_style_conditional.color +type = $track.track_file_style_conditional.display.display_selector +use summit = $track.track_file_style_conditional.display.use_summit +#if $track.track_file_style_conditional.display.display_selector == "peak": +show data range = $track.track_file_style_conditional.display.show_data +#if $track.track_file_style_conditional.display.width_adjust: +width adjust = $track.track_file_style_conditional.display.width_adjust +#end if +#if $track.track_file_style_conditional.display.min_value: +min_value = $track.track_file_style_conditional.display.min_value +#end if +#if $track.track_file_style_conditional.display.max_value: +max_value = $track.track_file_style_conditional.display.max_value +#end if +#end if + + +#if $track.track_file_style_conditional.height_narrow_peak: +height = $track.track_file_style_conditional.height_narrow_peak +#end if + +show labels = $track.track_file_style_conditional.show_labels + +file_type = narrow_peak +#if $track.track_file_style_conditional.fontsize: +fontsize = $track.track_file_style_conditional.fontsize +#end if + +#if $track.track_file_style_conditional.spacer_height != "": +[spacer] +height = $track.track_file_style_conditional.spacer_height +#end if +#end for +#end if + #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option": #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: @@ -271,9 +314,7 @@ max_value = auto #end if -#if $track.track_file_style_conditional.show_data: show data range = $track.track_file_style_conditional.show_data -#end if #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) #if $columns > 4: @@ -339,9 +380,7 @@ #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': type = points:$track.track_file_style_conditional.type_conditional.width_point #end if -#if $track.track_file_style_conditional.data_range: -show data range = $track.track_file_style_conditional.data_range -#end if +show data range = $track.track_file_style_conditional.show_data file_type = bigwig #if $track.track_file_style_conditional.invert_orientation: orientation = inverted @@ -430,6 +469,7 @@ <option value="chrom_states_option">Chromatine states</option> <option value="tad_score_track_option">TAD score</option> <option value="gene_track_option">Gene track / Bed track</option> + <option value="narrow_peak_track_option">NarrowPeak track</option> <option value="bigwig_track_option">Bigwig track</option> <option value="bedgraph_track_option">Bedgraph track </option> <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option> @@ -467,7 +507,7 @@ label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead of the matrix set to lines if a heatmap representing the matrix is not wanted"/> <param name="height_tad" type="float" value="0.2" optional="True" label="height"/> - <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> + <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range" /> <expand macro="spacer_macro" /> </when> @@ -504,6 +544,36 @@ <expand macro="spacer_macro" /> </when> + <when value="narrow_peak_track_option"> + <expand macro="plot_title" /> + <expand macro="track_input_narrow_peak_macro" /> + <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> + <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/> + <conditional name="display"> + <param name="display_selector" type="select" label="display to use"> + <option value="peak" selected="True">peak: Draw a peak shape from start, end, summit, height</option> + <option value="box">box: Draw a box</option> + </param> + <when value="peak"> + <param name='use_summit' type="boolean" truevalue="yes" falsevalue="no" checked="true" + optional="True" label="Use summit information to make the curve." /> + <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" + label="Show visualization of data range" /> + <param name='width_adjust' type="float" value="1.5" optional="True" + label="Factor to change the width of the curve."/> + <expand macro="minmax_macro" /> + </when> + <when value="box"> + <param name='use_summit' type="boolean" truevalue="yes" falsevalue="no" checked="true" + optional="True" label="Plot a vertical bar at the summit position." /> + </when> + </conditional> + <param name="show_labels" type="boolean" truevalue="yes" falsevalue="no" checked="true" + label="Plot labels (name, p-val, q-val)" /> + <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> + <expand macro="spacer_macro" /> + + </when> <when value="bedgraph_track_option"> <expand macro="plot_title" /> <expand macro="track_input_bedgraph_macro" /> @@ -511,7 +581,7 @@ <expand macro="minmax_macro" /> <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> <expand macro="type_coverage_macro" /> - <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> + <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range" /> <expand macro="inverted_macro" /> <expand macro="overlay_macro" /> <expand macro="spacer_macro" /> @@ -529,7 +599,7 @@ <expand macro="reading_bw_macro" /> <expand macro="type_coverage_macro" /> <expand macro="type_coverage_macro" /> - <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" label="Show visualization of data range"/> + <param name="show_data" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range"/> <expand macro="inverted_macro" /> <expand macro="overlay_macro" /> <expand macro="spacer_macro" /> @@ -969,7 +1039,9 @@ <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" /> <param name="height_bigwig" value="7" /> <param name="color" value="#00b0f0" /> - <param name="number_of_bins" value="2000"/> + <section name="reading_bw_conditional"> + <param name="number_of_bins" value="2000"/> + </section> </conditional> </repeat> <repeat name="tracks"> @@ -980,7 +1052,9 @@ <param name="color" value="#ff0000" /> <param name="alpha" value="0.5" /> <param name="summary" value="max" /> - <param name="number_of_bins" value="300"/> + <section name="reading_bw_conditional"> + <param name="number_of_bins" value="300"/> + </section> <param name="overlay_select" value="share-y"/> </conditional> </repeat> @@ -1017,6 +1091,62 @@ <param name="image_file_format" value="png" /> <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" /> </test> + <test> + <param name="region" value="X:2760000-2802000"/> + <conditional name="x_axis"> + <param name="x_axis_select" value="yes" /> + <param name="where" value="bottom" /> + </conditional> + <repeat name="tracks"> + <conditional name="track_file_style_conditional"> + <param name="track_file_style_selector" value="narrow_peak_track_option" /> + <param name="title" value="box" /> + <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> + <param name="color" value="#9bbb59" /> + <param name="height_narrow_peak" value="4" /> + <conditional name="display"> + <param name="display_selector" value="box" /> + <param name="use_summit" value="yes" /> + </conditional> + <param name="show_labels" value="yes" /> + </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" /> + <param name="height_narrow_peak" value="4" /> + <conditional name="display"> + <param name="display_selector" value="peak" /> + <param name="use_summit" value="yes" /> + <param name="show_data" value="yes" /> + <param name="width_adjust" value="3" /> + <param name="max_value" value="50" /> + </conditional> + <param name="show_labels" value="no" /> + <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="narrow_peak_track_option" /> + <param name="title" value="peak no data range" /> + <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> + <param name="color" value="#000000" /> + <param name="height_narrow_peak" value="4" /> + <conditional name="display"> + <param name="display_selector" value="peak" /> + <param name="use_summit" value="no" /> + <param name="show_data" value="no" /> + </conditional> + <param name="show_labels" value="yes" /> + </conditional> + </repeat> + <param name="image_file_format" value="png" /> + <output name="outFileName" file="test_narrowPeak.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/test2.narrowPeak Thu Sep 19 17:18:54 2019 -0400 @@ -0,0 +1,3 @@ +X 2763522 2773887 peak_14338 2505 . 37.31666 253.45494 250.59254 150 +X 2783479 2784861 peak_14339 1676 . 27.80457 170.24620 167.65807 1172 +X 2799191 2799443 peak_14341 885 . 17.74370 90.85378 88.53622 125