changeset 12:e4205fd3da4d draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cd4a8b019168acd5a513c57a1b1f380622f230f6
author bgruening
date Sun, 01 Jul 2018 03:20:35 -0400
parents 5621f2be9fbc
children af7c23a25c55
files clf_metrics.xml main_macros.xml test-data/feature_selection_result11 test-data/test3.tabular
diffstat 4 files changed, 118 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/clf_metrics.xml	Wed Jun 06 17:43:39 2018 -0400
+++ b/clf_metrics.xml	Sun Jul 01 03:20:35 2018 -0400
@@ -28,7 +28,7 @@
 
 header='infer' if params["clf_metrics"].get("header1", None) else None
 column_option = params["clf_metrics"]["column_selector_options_1"]["selected_column_selector_option"]
-if column_option in ["by_index_number", "all_but_by_index_number"]:
+if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
     c = params["clf_metrics"]["column_selector_options_1"]["col1"]
 else:
     c = None
@@ -43,7 +43,7 @@
 
 header='infer' if params["clf_metrics"].get("header2", None) else None
 column_option = params["clf_metrics"]["column_selector_options_2"]["selected_column_selector_option2"]
-if column_option in ["by_index_number", "all_but_by_index_number"]:
+if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
     c = params["clf_metrics"]["column_selector_options_2"]["col2"]
 else:
     c = None
--- a/main_macros.xml	Wed Jun 06 17:43:39 2018 -0400
+++ b/main_macros.xml	Sun Jul 01 03:20:35 2018 -0400
@@ -10,6 +10,12 @@
   if c_option == 'all_but_by_index_number':
     cols = list(map(lambda x: x - 1, c))
     data.drop(data.columns[cols], axis=1, inplace=True)
+  if c_option == 'by_header_name':
+    cols = [e.strip() for e in c.split(',')]
+    data = data[cols]
+  if c_option == 'all_but_by_header_name':
+    cols = [e.strip() for e in c.split(',')]
+    data.drop(cols, axis=1, inplace=True)
   y = data.values
   if return_df:
     return y, data
@@ -446,17 +452,23 @@
   <xml name="samples_column_selector_options" token_column_option="selected_column_selector_option" token_col_name="col1" token_multiple="False" token_infile="infile1">
     <param name="@COLUMN_OPTION@" type="select" label="Choose how to select data by column:">
       <option value="by_index_number" selected="true">Select columns by column index number(s)</option>
-      <!--<option value="by_header_name">Select columns by column header name(s)</option>-->
+      <option value="by_header_name">Select columns by column header name(s)</option>
       <option value="all_but_by_index_number">All columns but by column index number(s)</option>
-      <!--<option value="all_but_by_header_name">All columns but by column header name(s)</option> -->
+      <option value="all_but_by_header_name">All columns but by column header name(s)</option>
       <option value="all_columns">All columns</option>
     </param>
     <when value="by_index_number">
       <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" data_ref="@INFILE@" label="Select target column(s):"/>
     </when>
+    <when value="by_header_name">
+      <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="String seperate by colon. For example: target1,target2"/>
+    </when>
     <when value="all_but_by_index_number">
       <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" data_ref="@INFILE@" label="Select target column(s):"/>
     </when>
+    <when value="all_but_by_header_name">
+      <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="String seperate by colon. For example: target1,target2"/>
+    </when>
     <when value="all_columns">
     </when>
   </xml>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/feature_selection_result11	Sun Jul 01 03:20:35 2018 -0400
@@ -0,0 +1,51 @@
+Race	AIDS	Total
+4.0	2555.0	14443382.0
+4.0	55300.0	14704293.0
+4.0	82334.0	16641977.0
+4.0	38006.0	13888285.0
+4.0	16068.0	21845911.0
+2.0	2489.0	2367256.0
+2.0	34204.0	2410019.0
+2.0	51776.0	2727604.0
+2.0	23896.0	2276276.0
+2.0	10169.0	3580523.0
+3.0	1363.0	1542563.0
+3.0	20712.0	1570428.0
+3.0	27200.0	1777374.0
+3.0	11251.0	1483278.0
+3.0	4674.0	2333158.0
+1.0	38.0	699627.0
+1.0	731.0	712265.0
+1.0	1162.0	806125.0
+1.0	560.0	672738.0
+1.0	258.0	1058200.0
+0.0	26.0	169115.0
+0.0	390.0	172170.0
+0.0	417.0	194858.0
+0.0	140.0	162616.0
+0.0	48.0	255790.0
+4.0	490.0	14999423.0
+4.0	4788.0	15270378.0
+4.0	5377.0	17282659.0
+4.0	2152.0	14422956.0
+4.0	1790.0	22686934.0
+2.0	1490.0	2458391.0
+2.0	12280.0	2502800.0
+2.0	15713.0	2832611.0
+2.0	5788.0	2363908.0
+2.0	2534.0	3718366.0
+3.0	493.0	1601948.0
+3.0	4660.0	1630887.0
+3.0	5153.0	1845800.0
+3.0	1944.0	1540381.0
+3.0	910.0	2422980.0
+1.0	6.0	726561.0
+1.0	83.0	739686.0
+1.0	106.0	837159.0
+1.0	69.0	698637.0
+1.0	55.0	1098938.0
+0.0	3.0	175626.0
+0.0	78.0	178798.0
+0.0	77.0	202360.0
+0.0	31.0	168876.0
+0.0	14.0	265637.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test3.tabular	Sun Jul 01 03:20:35 2018 -0400
@@ -0,0 +1,51 @@
+Age	Race	AIDS	Total	target
+0	4	2555.0	14443382.0	1
+1	4	55300.0	14704293.0	1
+2	4	82334.0	16641977.0	1
+3	4	38006.0	13888285.0	1
+4	4	16068.0	21845911.0	1
+0	2	2489.0	2367256.0	1
+1	2	34204.0	2410019.0	1
+2	2	51776.0	2727604.0	1
+3	2	23896.0	2276276.0	1
+4	2	10169.0	3580523.0	1
+0	3	1363.0	1542563.0	1
+1	3	20712.0	1570428.0	1
+2	3	27200.0	1777374.0	1
+3	3	11251.0	1483278.0	1
+4	3	4674.0	2333158.0	1
+0	1	38.0	699627.0	1
+1	1	731.0	712265.0	1
+2	1	1162.0	806125.0	1
+3	1	560.0	672738.0	1
+4	1	258.0	1058200.0	1
+0	0	26.0	169115.0	1
+1	0	390.0	172170.0	1
+2	0	417.0	194858.0	1
+3	0	140.0	162616.0	1
+4	0	48.0	255790.0	1
+0	4	490.0	14999423.0	0
+1	4	4788.0	15270378.0	0
+2	4	5377.0	17282659.0	0
+3	4	2152.0	14422956.0	0
+4	4	1790.0	22686934.0	0
+0	2	1490.0	2458391.0	0
+1	2	12280.0	2502800.0	0
+2	2	15713.0	2832611.0	0
+3	2	5788.0	2363908.0	0
+4	2	2534.0	3718366.0	0
+0	3	493.0	1601948.0	0
+1	3	4660.0	1630887.0	0
+2	3	5153.0	1845800.0	0
+3	3	1944.0	1540381.0	0
+4	3	910.0	2422980.0	0
+0	1	6.0	726561.0	0
+1	1	83.0	739686.0	0
+2	1	106.0	837159.0	0
+3	1	69.0	698637.0	0
+4	1	55.0	1098938.0	0
+0	0	3.0	175626.0	0
+1	0	78.0	178798.0	0
+2	0	77.0	202360.0	0
+3	0	31.0	168876.0	0
+4	0	14.0	265637.0	0