| Previous changeset 1:09552faff9c0 (2015-08-17) Next changeset 3:f11a04ed443b (2016-03-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 70d4a2d1563e834d8394dce8017a1f0b7ad74f23 |
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modified:
taxonomy_krona_chart.xml test-data/krona_test1.html |
| b |
| diff -r 09552faff9c0 -r 50f204c82159 taxonomy_krona_chart.xml --- a/taxonomy_krona_chart.xml Mon Aug 17 11:36:09 2015 -0400 +++ b/taxonomy_krona_chart.xml Wed Mar 02 04:49:06 2016 -0500 |
| [ |
| @@ -1,7 +1,7 @@ -<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.0.0"> +<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.0"> <description>from taxonomic profile</description> <requirements> - <requirement type="package" version="2.5">krona</requirement> + <requirement type="package" version="2.6">krona</requirement> </requirements> <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command> <command> @@ -10,10 +10,9 @@ #if $type_of_data.input[0].is_of_type('taxonomy'): ktImportGalaxy - -a -d "${type_of_data.max_rank}" -n "${root_name}" - -o ${output} + -o "${output}" ${combine_inputs} #for $input_count, $input_dataset in enumerate( $type_of_data.input ): "${input_dataset},${input_count}" @@ -22,9 +21,8 @@ #else: ktImportText - -a -n "${root_name}" - -o ${output} + -o "${output}" ${combine_inputs} #for $input_count, $input_dataset in enumerate( $type_of_data.input ): "${input_dataset},${input_count}" @@ -32,6 +30,7 @@ #end if +&& [ -d "${output}.files" ] && ( mkdir "${output.extra_files_path}" && mv "${output}.files" "${output.extra_files_path}/" ) ]]> </command> @@ -72,7 +71,7 @@ <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" /> </when> </conditional> - <param name="root_name" type="text" size="20" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called "Root""/> + <param name="root_name" type="text" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called "Root""/> <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" selected="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/> </inputs> <outputs> @@ -94,7 +93,7 @@ This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_. -.. _Krona: http://sourceforge.net/p/krona/home/krona/ +.. _Krona: https://github.com/marbl/Krona/wiki ------ |
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| diff -r 09552faff9c0 -r 50f204c82159 test-data/krona_test1.html --- a/test-data/krona_test1.html Mon Aug 17 11:36:09 2015 -0400 +++ b/test-data/krona_test1.html Wed Mar 02 04:49:06 2016 -0500 |
| [ |
| b'@@ -76,7 +76,7 @@\n // \n // FOR MORE INFORMATION VISIT\n // \n-// http://krona.sourceforge.net\n+// https://github.com/marbl/Krona/wiki/\n // \n //-----------------------------------------------------------------------------\n }\n@@ -496,7 +496,77 @@\n \t\t\t}\n \t\t}\n \t\t\n-\t\tif ( this != selectedNode && ! this.getCollapse() )\n+\t\tif ( this.radial )\n+\t\t{\n+\t\t\tvar angleText = (angleStartCurrent + angleEndCurrent) / 2;\n+\t\t\tvar radiusText = (gRadius + radiusInner) / 2;\n+\t\t\t\n+\t\t\tcontext.rotate(angleText);\n+\t\t\tcontext.beginPath();\n+\t\t\tcontext.moveTo(radiusText, -fontSize);\n+\t\t\tcontext.lineTo(radiusText, fontSize);\n+\t\t\tcontext.lineTo(radiusText + centerX, fontSize);\n+\t\t\tcontext.lineTo(radiusText + centerX, -fontSize);\n+\t\t\tcontext.closePath();\n+\t\t\tcontext.rotate(-angleText);\n+\t\t\t\n+\t\t\tif ( context.isPointInPath(mouseX - centerX, mouseY - centerY) )\n+\t\t\t{\n+\t\t\t\tvar label = String(this.getPercentage()) + \'%\' + \' \' + this.name;\n+\t\t\t\t\n+\t\t\t\tif ( this.searchResultChildren() )\n+\t\t\t {\n+\t\t\t\t\tlabel += searchResultString(this.searchResultChildren());\n+\t\t\t\t}\n+\t\t\t\t\n+\t\t\t\tif\n+\t\t\t\t(\n+\t\t\t\t\tMath.sqrt((mouseX - centerX) * (mouseX - centerX) + (mouseY - centerY) * (mouseY - centerY)) <\n+\t\t\t\t\tradiusText + measureText(label)\n+\t\t\t\t)\n+\t\t\t\t{\n+\t\t\t\t\thighlighted = true;\n+\t\t\t\t}\n+\t\t\t}\n+\t\t}\n+\t\telse\n+\t\t{\n+\t\t for ( var i = 0; i < this.hiddenLabels.length; i++ )\n+\t\t {\n+\t\t var hiddenLabel = this.hiddenLabels[i];\n+\t\t \n+\t\t\t\tcontext.rotate(hiddenLabel.angle);\n+\t\t\t\tcontext.beginPath();\n+\t\t\t\tcontext.moveTo(gRadius, -fontSize);\n+\t\t\t\tcontext.lineTo(gRadius, fontSize);\n+\t\t\t\tcontext.lineTo(gRadius + centerX, fontSize);\n+\t\t\t\tcontext.lineTo(gRadius + centerX, -fontSize);\n+\t\t\t\tcontext.closePath();\n+\t\t\t\tcontext.rotate(-hiddenLabel.angle);\n+\t\t\t\t\n+\t\t\t\tif ( context.isPointInPath(mouseX - centerX, mouseY - centerY) )\n+\t\t\t\t{\n+\t\t\t\t\tvar label = String(hiddenLabel.value) + \' more\';\n+\t\t\t\t\t\n+\t\t\t\t\tif ( hiddenLabel.search )\n+\t\t\t\t {\n+\t\t\t\t\t\tlabel += searchResultString(hiddenLabel.search);\n+\t\t\t\t\t}\n+\t\t\t\t\t\n+\t\t\t\t\tif\n+\t\t\t\t\t(\n+\t\t\t\t\t\tMath.sqrt((mouseX - centerX) * (mouseX - centerX) + (mouseY - centerY) * (mouseY - centerY)) <\n+\t\t\t\t\t\tgRadius + fontSize + measureText(label)\n+\t\t\t\t\t)\n+\t\t\t\t\t{\n+\t\t\t\t\t\thighlighted = true;\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\t}\n+\t\t\t\t}\n+\t\t\t}\n+\t\t}\n+\t\t\n+\t\tif ( ! highlighted && this != selectedNode && ! this.getCollapse() )\n \t\t{\n \t\t\tcontext.beginPath();\n \t\t\tcontext.arc(0, 0, radiusInner, angleStartCurrent, angleEndCurrent, false);\n@@ -972,6 +1042,8 @@\n \t\t\t}\n \t\t}\n \t\t\n+\t\tthis.hiddenLabels = Array();\n+\t\t\n \t\tif ( drawChildren )\n \t\t{\n \t\t\t// draw children\n@@ -1122,6 +1194,14 @@\n \t\tvar textAngle = (angleStart + angleEnd) / 2;\n \t\tvar labelRadius = gRadius + fontSize;//(radiusInner + radius) / 2;\n \t\t\n+\t\tvar hiddenLabel = Array();\n+\t\t\n+\t\thiddenLabel.value = value;\n+\t\thiddenLabel.angle = textAngle;\n+\t\thiddenLabel.search = hiddenSearchResults;\n+\t\t\n+\t\tthis.hiddenLabels.push(hiddenLabel);\n+\t\t\n \t\tdrawTick(gRadius - fontSize * .75, fontSize * 1.5, textAngle);\n \t\tdrawTextPolar\n \t\t(\n@@ -2172,7 +2252,7 @@\n \t{\n \t\tvar nameWidthOld = this.nameWidth;\n \t\t\n-\t\tif ( ! this.radial )//&& fontSize != fontSizeLast )\n+\t\tif ( true || ! this.radial )//&& fontSize != fontSizeLast )\n \t\t{\n \t\t\tvar dim = context.measureText(this.name);\n \t\t\tthis.nameWidth = dim.width;\n@@ -3459,14 +3539,14 @@\n \t}\n \telse\n \t{\n-\t\tlogoImage = \'http://krona.sourceforge.net/img/logo.png\';\n+\t\tlogoImage = \'http://marbl.github.io/Krona/img/logo-small.png\';\n \t}\n \t\n //\tdocument.getElementById(\'options\').style.fontSize = \'9pt\';\n \tposition = addOptionElement\n \t(\n \t\tposition,\n-\'<a style="margin:2px" target="_blank" href="http://krona.sourceforge.net"><div style="display:inline-block;vertical-align:middle;background-color:#EEEEEE;border:1px solid gray;padding:2px;font-size:18px"><img style="vertical-align:middle;" src="\' + logoImage + \'"/><span style="vertical-align:middle;color:#555555">Krona</span></div></a><input type="button" id="back" value="←" title="Go back (Shortcut: ←)"/>\\\n+\'<a style="margin:2px" target="_blank" href="https://github.com/mar'..b'00</val><val>IA_1-45102</val><val>IA_1-45102</val><val>IA_1-48105</val><val>IA_1-48105</val><val>IA_1-57254</val><val>IA_1-61975</val><val>IA_1-61975</val><val>IA_1-66943</val><val>IA_1-68288</val><val>IA_1-82334</val><val>IA_1-95526</val></vals>\n+ </members>\n <rank><val>order</val></rank>\n- <node name="Sciurognathi">\n- <count><val>94</val></count>\n- <rank><val>suborder</val></rank>\n- <node name="Muridae">\n- <count><val>94</val></count>\n- <rank><val>family</val></rank>\n- <node name="Murinae">\n- <rank><val>subfamily</val></rank>\n- <count><val>94</val></count>\n- <node name="Rattus">\n- <rank><val>genus</val></rank>\n- <count><val>94</val></count>\n- <members>\n- <vals><val>IA_1-296315</val><val>IA_1-322295</val></vals>\n- </members>\n- <unassigned><val>2</val></unassigned>\n- <node name="Rattus norvegicus">\n- <rank><val>species</val></rank>\n- <count><val>92</val></count>\n- <members>\n- <vals><val>IA_1-144417</val><val>IA_1-278966</val><val>IA_1-314709</val><val>IA_1-324951</val><val>IA_1-27817</val><val>IA_1-95255</val><val>IA_1-104173</val><val>IA_1-135979</val><val>IA_1-139090</val><val>IA_1-139090</val><val>IA_1-139090</val><val>IA_1-144996</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-161439</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-216231</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-237681</val><val>IA_1-250166</val><val>IA_1-254274</val><val>IA_1-254274</val><val>IA_1-27817</val><val>IA_1-29000</val><val>IA_1-291427</val><val>IA_1-291427</val><val>IA_1-293054</val><val>IA_1-293054</val><val>IA_1-296315</val><val>IA_1-310974</val><val>IA_1-310974</val><val>IA_1-311282</val><val>IA_1-311282</val><val>IA_1-42600</val><val>IA_1-45102</val><val>IA_1-45102</val><val>IA_1-48105</val><val>IA_1-48105</val><val>IA_1-57254</val><val>IA_1-61975</val><val>IA_1-61975</val><val>IA_1-66943</val><val>IA_1-68288</val><val>IA_1-82334</val><val>IA_1-95526</val></vals>\n- </members>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n+ <count><val>94</val></count>\n </node>\n </node>\n </node>\n@@ -6582,8 +6638,8 @@\n </node>\n </node>\n <node name="Bacteria">\n+ <count><val>6</val></count>\n <rank><val>superkingdom</val></rank>\n- <count><val>6</val></count>\n <node name="Proteobacteria">\n <count><val>6</val></count>\n <rank><val>phylum</val></rank>\n@@ -6597,8 +6653,8 @@\n <count><val>6</val></count>\n <rank><val>family</val></rank>\n <node name="Shigella">\n+ <count><val>6</val></count>\n <rank><val>genus</val></rank>\n- <count><val>6</val></count>\n <node name="Shigella flexneri">\n <count><val>6</val></count>\n <rank><val>species</val></rank>\n' |