Mercurial > repos > jjohnson > pandas_pivot_table
comparison pandas_pivot_table.xml @ 3:4b65133e0722 draft
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit e0560d99fd88685476e4b65235b89edeb20e8426-dirty"
| author | jjohnson |
|---|---|
| date | Thu, 17 Dec 2020 22:23:11 +0000 |
| parents | 6f05390deffa |
| children | eaf2444a2a50 |
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| 2:6f05390deffa | 3:4b65133e0722 |
|---|---|
| 1 <tool id="pandas_pivot_table" name="Pivot Table" version="@VERSION@.0" python_template_version="3.5"> | 1 <tool id="pandas_pivot_table" name="Pivot Table" version="@VERSION@.1" python_template_version="3.5"> |
| 2 <description>transform tabular data</description> | 2 <description>transform tabular data</description> |
| 3 <macros> | 3 <macros> |
| 4 <token name="@VERSION@">1.1.4</token> | 4 <token name="@VERSION@">1.1.4</token> |
| 5 <token name="@AGGFUNC@">'(min|max|sum|size|count|mean|std|var|prod|all|any)'</token> | |
| 6 <token name="@AGGFUNCS@">(@AGGFUNC@|[[]\s*@AGGFUNC@(,\s*@AGGFUNC@)*])</token> | |
| 7 <token name="@AGGITEM@">'\S+'\s*:\s*@AGGFUNCS@</token> | |
| 8 <token name="@AGGDICT@">{@AGGITEM@(,\s*@AGGITEM@)*}</token> | |
| 9 <token name="@AGGF@">(@AGGFUNCS@|@AGGDICT@)</token> | |
| 5 </macros> | 10 </macros> |
| 6 <requirements> | 11 <requirements> |
| 7 <requirement type="package" version="@VERSION@">pandas</requirement> | 12 <requirement type="package" version="@VERSION@">pandas</requirement> |
| 8 </requirements> | 13 </requirements> |
| 9 <command detect_errors="exit_code"><![CDATA[ | 14 <command detect_errors="exit_code"><![CDATA[ |
| 17 --header $header.names | 22 --header $header.names |
| 18 #end if | 23 #end if |
| 19 --index '$pvt_index' | 24 --index '$pvt_index' |
| 20 --columns '$pvt_columns' | 25 --columns '$pvt_columns' |
| 21 --values '$pvt_values' | 26 --values '$pvt_values' |
| 22 --aggfunc='$aggfunc' | 27 --aggfunc="$aggfunc" |
| 23 #if $fill_value | 28 #if $fill_value |
| 24 --fill_value '$fill_value' | 29 --fill_value '$fill_value' |
| 25 #end if | 30 #end if |
| 26 #if $float_format | 31 #if $float_format |
| 27 --float_format '$float_format' | 32 --float_format '$float_format' |
| 58 </param> | 63 </param> |
| 59 <param name="pvt_values" type="text" value="" label="Pivot table value columns"> | 64 <param name="pvt_values" type="text" value="" label="Pivot table value columns"> |
| 60 <validator type="regex" message="Column names separated by commas">^\S+(,\S+)*$</validator> | 65 <validator type="regex" message="Column names separated by commas">^\S+(,\S+)*$</validator> |
| 61 </param> | 66 </param> |
| 62 <param name="aggfunc" type="text" value="" label="Pivot table aggregate function"> | 67 <param name="aggfunc" type="text" value="" label="Pivot table aggregate function"> |
| 63 <help><![CDATA[A valid JSON string, e.g.: | 68 <help><![CDATA[ |
| 64 <ul> | 69 <ul> |
| 65 <li>A single function applied to each <i>value</i> column: <b>"min"</b></li> | 70 <li>Available Number Functions: @AGGFUNC@</li> |
| 66 <li>An array of functions applied to each <i>value</i> column: <b>["min", "max", "mean", "std"]</b></li> | 71 <li>Specify functions as (remember the single quotes):</li> |
| 67 <li>A dictionary of <i>value column : function(s)</i>: <b>{"A" : "sum", "B" : ["min", "max"]}</b></li> | 72 <ul> |
| 68 </ul> | 73 <li> - A single function applied to each <i>value</i> column: <b>'min'</b></li> |
| 74 <li> - An array of functions applied to each <i>value</i> column: <b>['min', 'max', 'mean', 'std']</b></li> | |
| 75 <li> - A dictionary of <i>value column : function(s)</i>: <b>{'A' : 'sum', 'B' : ['min', 'max']}</b></li> | |
| 76 </ul> | |
| 77 </ul> | |
| 69 ]]></help> | 78 ]]></help> |
| 70 <validator type="regex" message="Do not forget the double quotes">.*".+".*</validator> | 79 <validator type="regex" message="Do not forget the single quotes">@AGGF@</validator> |
| 71 <sanitizer> | 80 <sanitizer> |
| 72 <valid initial="string.printable"> | 81 <valid initial="string.printable"> |
| 73 <remove value="'"/> | |
| 74 </valid> | 82 </valid> |
| 75 <mapping initial="none"> | |
| 76 <add source="'" target="__sq__"/> | |
| 77 </mapping> | |
| 78 </sanitizer> | 83 </sanitizer> |
| 79 </param> | 84 </param> |
| 80 <param name="fill_value" type="text" value="" optional="true" label="Fill value (optional)" | 85 <param name="fill_value" type="text" value="" optional="true" label="Fill value (optional)" |
| 81 help="Value to replace missing values with (in the resulting pivot table, after aggregation) default is an empty field"/> | 86 help="Value to replace missing values with (in the resulting pivot table, after aggregation) default is an empty field"/> |
| 82 <param name="float_format" type="text" value="" optional="true" label="Output floating point format (optional)"> | 87 <param name="float_format" type="text" value="" optional="true" label="Output floating point format (optional)"> |
| 83 <help>Default is six decimal places: %0.6f</help> | 88 <help><![CDATA[Default is six decimal places: <i>%0.<b>6</b>f</i> For scientific: <i>%0.6<b>e</b></i>]]></help> |
| 84 <validator type="regex" message="">^%\d+.\d+[fFeEgGn]$</validator> | 89 <validator type="regex" message="%0.6f">^%\d+.\d+[fFeEgGn]$</validator> |
| 85 <sanitizer> | 90 <sanitizer> |
| 86 <valid initial="string.digits"> | 91 <valid initial="string.digits"> |
| 87 <add value="%" /> | 92 <add value="%" /> |
| 88 <add value="." /> | 93 <add value="." /> |
| 89 <add value="f" /> | 94 <add value="f" /> |
| 107 <param name="header_choice" value="first_line"/> | 112 <param name="header_choice" value="first_line"/> |
| 108 </conditional> | 113 </conditional> |
| 109 <param name="pvt_index" value="A" /> | 114 <param name="pvt_index" value="A" /> |
| 110 <param name="pvt_columns" value="C"/> | 115 <param name="pvt_columns" value="C"/> |
| 111 <param name="pvt_values" value="D"/> | 116 <param name="pvt_values" value="D"/> |
| 112 <param name="aggfunc" value=""max""/> | 117 <param name="aggfunc" value="'max'"/> |
| 113 <output name="output"> | 118 <output name="output"> |
| 114 <assert_contents> | 119 <assert_contents> |
| 115 <has_text_matching expression="bar\t7\t6" /> | 120 <has_text_matching expression="bar\t7\t6" /> |
| 116 </assert_contents> | 121 </assert_contents> |
| 117 </output> | 122 </output> |
| 122 <param name="header_choice" value="first_line"/> | 127 <param name="header_choice" value="first_line"/> |
| 123 </conditional> | 128 </conditional> |
| 124 <param name="pvt_index" value="A" /> | 129 <param name="pvt_index" value="A" /> |
| 125 <param name="pvt_columns" value="C"/> | 130 <param name="pvt_columns" value="C"/> |
| 126 <param name="pvt_values" value="D"/> | 131 <param name="pvt_values" value="D"/> |
| 127 <param name="aggfunc" value="["min","max"]"/> | 132 <param name="aggfunc" value="['min','max']"/> |
| 128 <output name="output"> | 133 <output name="output"> |
| 129 <assert_contents> | 134 <assert_contents> |
| 130 <has_text_matching expression="bar\t4\t5\t7\t6" /> | 135 <has_text_matching expression="bar\t4\t5\t7\t6" /> |
| 131 </assert_contents> | 136 </assert_contents> |
| 132 </output> | 137 </output> |
| 137 <param name="header_choice" value="first_line"/> | 142 <param name="header_choice" value="first_line"/> |
| 138 </conditional> | 143 </conditional> |
| 139 <param name="pvt_index" value="C,B" /> | 144 <param name="pvt_index" value="C,B" /> |
| 140 <param name="pvt_columns" value="A"/> | 145 <param name="pvt_columns" value="A"/> |
| 141 <param name="pvt_values" value="D,E"/> | 146 <param name="pvt_values" value="D,E"/> |
| 142 <param name="aggfunc" value="{"D" : ["min","sum"], "E" : "mean"}"/> | 147 <param name="aggfunc" value="{'D' : ['min','sum'], 'E' : 'mean'}"/> |
| 143 <output name="output"> | 148 <output name="output"> |
| 144 <assert_contents> | 149 <assert_contents> |
| 145 <has_text_matching expression="C\tB\tbar_min_D\tfoo_min_D\tbar_sum_D\tfoo_sum_D\tbar_mean_E\tfoo_mean_E"/> | 150 <has_text_matching expression="C\tB\tbar_min_D\tfoo_min_D\tbar_sum_D\tfoo_sum_D\tbar_mean_E\tfoo_mean_E"/> |
| 146 <has_text_matching expression="large\tone\t4[.]\d+\t2[.]\d+\t4[.]\d+\t4[.]\d+\t6[.]\d+\t4[.]5\d+"/> | 151 <has_text_matching expression="large\tone\t4[.]\d+\t2[.]\d+\t4[.]\d+\t4[.]\d+\t6[.]\d+\t4[.]5\d+"/> |
| 147 </assert_contents> | 152 </assert_contents> |