| Previous changeset 3:feab9265552d (2019-08-26) Next changeset 5:eca03db4f612 (2020-01-08) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" |
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modified:
macros.xml pyGenomeTracks.xml test-data/bigwig_multiple.png test-data/master_TADs_BW_plot.png test-data/master_TADs_plot.png test-data/test_alpha.png |
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added:
test-data/test2.narrowPeak test-data/test_narrowPeak.png |
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removed:
test-data/bigwig_multiple_before.png test-data/master_TADs_plot_before.png |
| b |
| diff -r feab9265552d -r c237ba772225 macros.xml --- a/macros.xml Mon Aug 26 06:20:55 2019 -0400 +++ b/macros.xml Thu Sep 19 17:18:54 2019 -0400 |
| b |
| @@ -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> |
| b |
| diff -r feab9265552d -r c237ba772225 pyGenomeTracks.xml --- a/pyGenomeTracks.xml Mon Aug 26 06:20:55 2019 -0400 +++ b/pyGenomeTracks.xml Thu Sep 19 17:18:54 2019 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.2">\n+<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.1">\n <description>plot genomic data tracks</description>\n <macros>\n <token name="@BINARY@">pyGenomeTracks</token>\n@@ -129,9 +129,7 @@\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.show_data:\n show data range = $track.track_file_style_conditional.show_data\n-#end if\n \n #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split(\'\\t\'))\n #if $columns > 4:\n@@ -239,6 +237,51 @@\n #end for\n #end if\n \n+#if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option":\n+#for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak):\n+\n+[narrow_peak_${counter}_${counter_narrow_peak}]\n+file = $data_narrow_peak\n+#if $track.track_file_style_conditional.title:\n+title = $track.track_file_style_conditional.title\n+#else:\n+title = $data_narrow_peak.name\n+#end if\n+color = $track.track_file_style_conditional.color\n+type = $track.track_file_style_conditional.display.display_selector\n+use summit = $track.track_file_style_conditional.display.use_summit\n+#if $track.track_file_style_conditional.display.display_selector == "peak":\n+show data range = $track.track_file_style_conditional.display.show_data\n+#if $track.track_file_style_conditional.display.width_adjust:\n+width adjust = $track.track_file_style_conditional.display.width_adjust\n+#end if\n+#if $track.track_file_style_conditional.display.min_value:\n+min_value = $track.track_file_style_conditional.display.min_value\n+#end if\n+#if $track.track_file_style_conditional.display.max_value:\n+max_value = $track.track_file_style_conditional.display.max_value\n+#end if\n+#end if\n+\n+\n+#if $track.track_file_style_conditional.height_narrow_peak:\n+height = $track.track_file_style_conditional.height_narrow_peak\n+#end if\n+\n+show labels = $track.track_file_style_conditional.show_labels\n+\n+file_type = narrow_peak\n+#if $track.track_file_style_conditional.fontsize:\n+fontsize = $track.track_file_style_conditional.fontsize\n+#end if\n+\n+#if $track.track_file_style_conditional.spacer_height != "":\n+[spacer]\n+height = $track.track_file_style_conditional.spacer_height\n+#end if\n+#end for\n+#end if\n+\n \n #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":\n #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:\n@@ -271,9 +314,7 @@\n max_value = auto\n #end if\n \n-#if $track.track_file_style_conditional.show_data:\n show data range = $track.track_file_style_conditional.show_data\n-#end if\n \n #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split(\'\\t\'))\n #if $columns > 4:\n@@ -339,9 +380,7 @@\n #elif $track.track_file_style_conditional.type_conditional.type_selector == \'point_option\':\n type = points:$track.track_file_style_conditional.type_conditional.width_point\n #end if\n-#if $track.track_file_style_conditional.data_range:\n-show data range = $track.track_file_style_conditional.data_range\n-#end if\n+show data range = $track.track_file_style_conditional.show_data\n file_type = bigwig\n #if $track.track_file_style_conditional.invert_orientation:\n orientation = inverted\n@@ -430,6 +469,7 @@\n <option value="chrom_states_option">Chromatine states</option>\n <option value="tad_score_track_option">TAD score</option>\n <option value="gene_track_option">Gene track / Bed track</option>\n+ <option value="narrow_peak_track_option">NarrowPeak track</option>\n <option value="bigwig_track_option">Bigwig track</option>\n <option value="bedgraph_track_option">Bedgraph track </option>\n <option value="be'..b'00" />\n <param name="alpha" value="0.5" />\n <param name="summary" value="max" />\n- <param name="number_of_bins" value="300"/>\n+ <section name="reading_bw_conditional">\n+ <param name="number_of_bins" value="300"/>\n+ </section>\n <param name="overlay_select" value="share-y"/>\n </conditional>\n </repeat>\n@@ -1017,6 +1091,62 @@\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+ <test>\n+ <param name="region" value="X:2760000-2802000"/>\n+ <conditional name="x_axis">\n+ <param name="x_axis_select" value="yes" />\n+ <param name="where" value="bottom" />\n+ </conditional>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="narrow_peak_track_option" />\n+ <param name="title" value="box" />\n+ <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />\n+ <param name="color" value="#9bbb59" />\n+ <param name="height_narrow_peak" value="4" />\n+ <conditional name="display">\n+ <param name="display_selector" value="box" />\n+ <param name="use_summit" value="yes" />\n+ </conditional>\n+ <param name="show_labels" value="yes" />\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="narrow_peak_track_option" />\n+ <param name="title" value="peak width 3" />\n+ <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />\n+ <param name="color" value="#c0504d" />\n+ <param name="height_narrow_peak" value="4" />\n+ <conditional name="display">\n+ <param name="display_selector" value="peak" />\n+ <param name="use_summit" value="yes" />\n+ <param name="show_data" value="yes" />\n+ <param name="width_adjust" value="3" />\n+ <param name="max_value" value="50" />\n+ </conditional>\n+ <param name="show_labels" value="no" />\n+ <param name="spacer_height" value="0.5"/>\n+ </conditional>\n+ </repeat>\n+ <repeat name="tracks">\n+ <conditional name="track_file_style_conditional">\n+ <param name="track_file_style_selector" value="narrow_peak_track_option" />\n+ <param name="title" value="peak no data range" />\n+ <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />\n+ <param name="color" value="#000000" />\n+ <param name="height_narrow_peak" value="4" />\n+ <conditional name="display">\n+ <param name="display_selector" value="peak" />\n+ <param name="use_summit" value="no" />\n+ <param name="show_data" value="no" />\n+ </conditional>\n+ <param name="show_labels" value="yes" />\n+ </conditional>\n+ </repeat>\n+ <param name="image_file_format" value="png" />\n+ <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" />\n+ </test>\n </tests>\n <help><
