Mercurial > repos > jjohnson > column_join
diff column_join.xml @ 0:6bb6c0a30c67 draft default tip
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| author | jjohnson |
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| date | Tue, 01 Apr 2014 09:30:45 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/column_join.xml Tue Apr 01 09:30:45 2014 -0400 @@ -0,0 +1,260 @@ +<tool id="column_join" name="Column Join" version="1.1.0"> + <description></description> + <command interpreter="python"> + column_join.py + --output=$output + --input1=$input1 + --input2=$input2 + --hinge=$hinge + --columns=$columns + #if $fill_empty_columns.fill_empty_columns_switch == "fill_empty": + --fill_options_file=$fill_options_file + #end if + #for $f in $file_chooser: + ${f.input} + #end for + </command> + <inputs> + <param name="input1" type="data" format="tabular" label="Choose the first file for the join" /> + <param name="hinge" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Use this column and columns to left the 'hinge' (matching data for each join)" help="All columns to left of selected column (plus selected column) will be used. Select 2 for pileup" /> + <param name="columns" type="data_column" data_ref="input1" multiple="true" numerical="false" label="Include these column" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" /> + <conditional name="fill_empty_columns"> + <param name="fill_empty_columns_switch" type="select" label="Fill empty columns"> + <option value="no_fill" selected="True">No</option> + <option value="fill_empty">Yes</option> + </param> + <when value="no_fill" /> + <when value="fill_empty"> + <conditional name="do_fill_empty_columns"> + <param name="column_fill_type" type="select" label="Fill Columns by"> + <option value="single_fill_value" selected="True">Single fill value</option> + <option value="fill_value_by_column">Values by column</option> + </param> + <when value="single_fill_value"> + <param type="text" name="fill_value" label="Fill value" value="." /> + </when> + <when value="fill_value_by_column"> + <repeat name="column_fill" title="Fill Column"> + <param name="column_number" label="Column" type="data_column" data_ref="input1" /> + <param type="text" name="fill_value" value="." /> + </repeat> + </when> + </conditional> + </when> + </conditional> + <param name="input2" type="data" format="tabular" label="Choose the second file for the join" /> + <repeat name="file_chooser" title="Additional Input"> + <param name="input" label="Additional input file" type="data" format="tabular" /> + </repeat> + </inputs> + <configfiles> + <configfile name="fill_options_file"><% +import json +%> +#set $__fill_options = {} +#if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty': + #if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'single_fill_value': + #set $__start_fill = $fill_empty_columns['do_fill_empty_columns']['fill_value'].value + #else: + #set $__start_fill = "" + #end if + #set $__fill_options['file1_columns'] = [ __start_fill for i in range( int( $input1.metadata.columns ) ) ] + #if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'fill_value_by_column': + #for column_fill in $fill_empty_columns['do_fill_empty_columns']['column_fill']: + #set $__fill_options['file1_columns'][ int( column_fill['column_number'].value ) - 1 ] = column_fill['fill_value'].value + #end for + #end if +#end if +${json.dumps( __fill_options )} + </configfile> + </configfiles> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input1" value="column_join_in1.pileup" ftype="pileup" /> + <param name="hinge" value="2" /> + <param name="columns" value="1,2,3,4,5,7" /> + <param name="fill_empty_columns_switch" value="fill_empty" /> + <param name="column_fill_type" value="single_fill_value" /> + <param name="fill_value" value="?" /> + <param name="input2" value="column_join_in2.pileup" ftype="pileup" /> + <param name="input" value="column_join_in3.pileup" ftype="pileup" /> + <output name="output" file="column_join_out1.pileup" ftype="tabular" /> + </test> + <test> + <param name="input1" value="column_join_in4.pileup" ftype="pileup" /> + <param name="hinge" value="2" /> + <param name="columns" value="1,2,3,4" /> + <param name="fill_empty_columns_switch" value="no_fill" /> + <param name="input2" value="column_join_in5.pileup" ftype="pileup" /> + <param name="input" value="column_join_in6.pileup" ftype="pileup" /> + <output name="output" file="column_join_out2.pileup" ftype="tabular" /> + </test> +<!-- This test is failing for an unclear reason (the column values do not get + passed into the script), but passes in the browser + <test> + <param name="input1" value="column_join_in7.pileup" ftype="tabular" /> + <param name="hinge" value="2" /> + <param name="columns" value="3,4,5" /> + <param name="fill_empty_columns_switch" value="fill_empty" /> + <param name="column_fill_type" value="fill_value_by_column" /> + <param name="column_number" value="5" /> + <param name="fill_value" value="X" /> + <param name="input2" value="column_join_in8.pileup" ftype="tabular" /> + <param name="input" value="column_join_in9.pileup" ftype="tabular" /> + <output name="output" file="column_join_out3.pileup" ftype="tabular" /> + </test> +--> + <test> + <param name="input1" value="column_join_in10.pileup" ftype="pileup" /> + <param name="hinge" value="1" /> + <param name="columns" value="2,7" /> + <param name="fill_empty_columns_switch" value="no_fill" /> + <param name="input2" value="column_join_in11.pileup" ftype="pileup" /> + <param name="input" value="column_join_in12.pileup" ftype="pileup" /> + <output name="output" file="column_join_out4.pileup" ftype="tabular" /> + </test> + <test> + <!-- Test for handling missing column --> + <param name="input1" value="column_join_in13.tabular" ftype="tabular" /> + <param name="hinge" value="1" /> + <param name="columns" value="5" /> + <param name="fill_empty_columns_switch" value="fill_empty" /> + <param name="column_fill_type" value="single_fill_value" /> + <param name="fill_value" value="0" /> + <param name="input2" value="column_join_in14.tabular" ftype="tabular" /> + <param name="input" value="column_join_in15.tabular" ftype="tabular" /> + <output name="output" file="column_join_out5.tabular" ftype="tabular" /> + </test> + </tests> + <help> +**What it does** + +This tool allows you to join several files with the same column structure into one file, removing certain columns if necessary. The user needs to select a 'hinge', which is the number of left-most columns to match on. They also need to select the columns to include in the join, which should include the hinge columns, too. + +Note that the files are expected to have the same number of columns. If for some reason the join column is missing (this only applies to the last column(s)), the tool attempts to handle this situation by inserting an empty item (or the appropriate filler) for that column on that row. This could lead to the situation where a row has a hinge but entirely empty or filled columns, if the hinge exists in at least one file but every file that has it is missing the join column. Also, note that the tool does not distinguish between a file missing the hinge altogether and a file having the hinge but missing the column (in both cases the column would be empty or filled). There is an example of this below. + +----- + +**General Example** + +Given the following files:: + + FILE 1 + chr2 1 T 6 .C..., I$$III + chr2 2 G 6 ..N.., III@II + chr2 3 C 7 ..C..., I$IIIII + chr2 4 G 7 .G...., I#IIIII + chr2 5 G 7 ...N.., IIII#BI + chr2 6 A 7 ..T..., I$IDIII + chr1 1 C 1 ^:. I + chr1 2 G 2 .^:. $I + chr1 3 A 2 .. I% + chr1 4 C 2 .. I$ + chr1 5 T 3 ..^:. I#I + chr1 6 G 3 ..^:, I#I + + FILE 2 + chr1 3 T 1 ^:. I + chr1 4 G 2 .^:. $I + chr1 5 T 2 .. I% + chr1 6 C 3 ..^:. III + chr1 7 G 3 ..^:. I#I + chr1 8 T 4 ...^:, I#II + chr2 77 C 6 .G..., I$$III + chr2 78 G 6 ..N.., III@II + chr2 79 T 7 ..N..., I$IIIII + chr2 80 C 7 .G...., I#IIIII + chr2 81 G 7 ...A.., IIII#BI + chr2 82 A 8 ...G..., I$IDIIII + chr2 83 T 8 .A.....N IIIIIIII + chr2 84 A 9 ......T. I$IIIIIII + + FILE 3 + chr1 1 A 1 . I + chr1 2 T 2 G. I$ + chr1 3 C 2 ., I@ + chr1 4 C 3 ..N III + chr1 42 C 5 ...N^:. III@I + chr1 43 C 5 .N..^:. IIIII + chr1 44 T 5 .A.., IA@II + chr1 45 A 6 .N...^:. IIIII$ + chr1 46 G 6 .GN..^:. I@IIII + chr1 47 A 7 ....^:.., IIIII$I + chr2 73 T 5 .N.., II$II + chr2 74 A 5 ...., IIIII + chr2 75 T 5 ...., IIIII + chr2 76 T 5 ...., IIIII + chr2 77 C 5 ...., IIIBI + chr2 78 T 5 ...., IDIII + +To join on columns 3 and 4 combining on columns 1 and 2, columns 1-4 should be selected for the 'Include these columns' option, and column 2 selected for the 'hinge'. With these settings, the following would be output:: + + chr1 1 C 1 A 1 + chr1 2 G 2 T 2 + chr1 3 A 2 T 1 C 2 + chr1 4 C 2 G 2 C 3 + chr1 5 T 3 T 2 + chr1 6 G 3 C 3 + chr1 7 G 3 + chr1 8 T 4 + chr1 42 C 5 + chr1 43 C 5 + chr1 44 T 5 + chr1 45 A 6 + chr1 46 G 6 + chr1 47 A 7 + chr2 1 T 6 + chr2 2 G 6 + chr2 3 C 7 + chr2 4 G 7 + chr2 5 G 7 + chr2 6 A 7 + chr2 73 T 5 + chr2 74 A 5 + chr2 75 T 5 + chr2 76 T 5 + chr2 77 C 6 C 5 + chr2 78 G 6 T 5 + chr2 79 T 7 + chr2 80 C 7 + chr2 81 G 7 + chr2 82 A 8 + chr2 83 T 8 + chr2 84 A 9 + +**Example with missing columns** + +Given the following input files:: + + FILE 1 + 1 A + 2 B b + 4 C c + 5 D + 6 E e + + FILE 2 + 1 M m + 2 N + 3 O o + 4 P p + 5 Q + 7 R r + +if we join only column 3 using column 1 as the hinge and with a fill value of '0', this is what will be output:: + + 1 0 m + 2 b 0 + 3 0 o + 4 c p + 5 0 0 + 6 e 0 + 7 0 r + +Row 5 appears in both files with the missing column, so it's got nothing but fill values in the output file. + + </help> +</tool>