column_maker: column_maker.xml annotate

annotate column_maker.xml @ 9:33b81f9ea109 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7

author	iuc
date	Thu, 28 Jul 2022 15:27:54 +0000
parents	227e82286a0e
children	beec6ecc7d3c

rev	line source
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	1 <tool id="Add_a_column1" name="Compute" version="2.0">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	2 <description>on rows</description>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	3 <macros>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	4 <xml name="compute_repeat">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	5 <repeat name="expressions" title="Expressions" min="1" default="1">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	6 <param name="cond" type="text" value="c3-c2" label="Add expression">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	7 <sanitizer>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	8 <valid initial="default">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	9 <add value="<" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	10 <add value=">" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	11 <add value=""" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	12 <add value="'" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	13 </valid>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	14 </sanitizer>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	15 </param>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	16 <conditional name="add_column">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	17 <param name="mode" type="select" label="Mode of the operation">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	18 <option value="">Append</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	19 <option value="I">Insert</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	20 <option value="R">Replace</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	21 </param>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	22 <when value="">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	23 <param name="pos" type="hidden" value="" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	24 </when>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	25 <when value="I">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	26 <param name="pos" type="integer" min="1" value="1" label="Insert new column before existing column number" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	27 </when>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	28 <when value="R">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	29 <param name="pos" type="integer" min="1" value="1" label="Use new column to replace column number" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	30 </when>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	31 </conditional>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	32 <yield />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	33 </repeat>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	34 </xml>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	35 </macros>
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	36 <requirements>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	37 <requirement type="package" version="3.8">python</requirement>
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	38 <requirement type="package" version="1.23.1">numpy</requirement>
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	39 </requirements>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	40 <command detect_errors="aggressive"><![CDATA[
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	41 python '$__tool_directory__/column_maker.py'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	42 #if str($error_handling.auto_col_types) == 'on':
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	43 #set $col_types = $input.metadata.column_types
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	44 #else:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	45 #set $col_types = ','.join(['str' for t in $input.metadata.column_types.split(',')])
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	46 #end if
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	47 --column-types $col_types
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	48 $avoid_scientific_notation
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	49 #if str($ops.header_lines_select) == 'yes':
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	50 --header
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	51 #end if
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	52 --file '$expressions_file'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	53 $error_handling.fail_on_non_existent_columns
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	54 $error_handling.non_computable.action
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	55 #if str($error_handling.non_computable.action) == '--non-computable-default':
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	56 '$error_handling.non_computable.default_value'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	57 #end if
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	58 '$input'
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	59 '$out_file1'
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	60 ]]></command>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	61 <configfiles>
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	62 <configfile name="expressions_file"><![CDATA[
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	63 #if str($ops.header_lines_select) == 'yes':
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	64 #for $expr in $ops.expressions:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	65 ${expr.cond};${expr.add_column.pos}${expr.add_column.mode};${expr.new_column_name}
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	66 #end for
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	67 #else:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	68 #for $expr in $ops.expressions:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	69 ${expr.cond};${expr.add_column.pos}${expr.add_column.mode};
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	70 #end for
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	71 #end if
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	72 ]]></configfile>
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	73 </configfiles>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	74 <inputs>
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	75 <param name="input" type="data" format="tabular" label="Input file" help="Dataset missing? See TIP below" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	76 <conditional name="ops">
7 e7c273e8d4d6 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187" devteam parents: 6 diff changeset	77 <param name="header_lines_select" type="select"
e7c273e8d4d6 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187" devteam parents: 6 diff changeset	78 label="Input has a header line with column names?"
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	79 help="Select Yes to be able to specify names for new columns and have them added to the header line. If you select No, the first line will be treated as a regular line: If it is empty or starts with a # character it will be skipped, otherwise the tool will attempt to compute the specified expression on it." >
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	80 <option value="no">No</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	81 <option value="yes">Yes</option>
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	82 </param>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	83 <when value="no">
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	84 <expand macro="compute_repeat" />
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	85 </when>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	86 <when value="yes">
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	87 <expand macro="compute_repeat">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	88 <param name="new_column_name" type="text" value="New Column" label="The new column name" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	89 </expand>
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	90 </when>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	91 </conditional>
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	92 <param name="avoid_scientific_notation" type="boolean" truevalue="--avoid-scientific-notation" falsevalue=""
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	93 label="Avoid scientific notation in any newly computed columns"
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	94 help="If yes, use fully expanded decimal representation when writing new columns with floating point values. To prevent scientific notation in just specific new columns, you can use numpy's format_float_positional function in the corresponding expression." />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	95 <section name="error_handling" title="Error handling">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	96 <param name="auto_col_types" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Autodetect column types"
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	97 help="By default, try to use the column types that Galaxy has recorded for the input. This simplifies expressions, but can occasionally cause problems on its own. If disabled all column values are assumed to be strings and you will have to handle conversions to different types explicitly in the expression." />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	98 <param argument="--fail-on-non-existent-columns" type="boolean" truevalue="--fail-on-non-existent-columns" falsevalue="" checked="true" label="Fail on references to non-existent columns"
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	99 help="If any expression references a column number that does not exist when that expression gets computed, the tool run will fail. Uncheck to have such a situation handled as a case of a non-computable expression as configured below." />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	100 <conditional name="non_computable">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	101 <param name="action" type="select" label="If an expression cannot be computed for a row">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	102 <option value="--fail-on-non-computable">Fail the entire tool run</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	103 <option value="--skip-non-computable">Skip the row</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	104 <option value="--keep-non-computable">Keep the row unchanged</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	105 <option value="--non-computable-blank">Produce an empty column value for the row</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	106 <option value="--non-computable-default">Fill in a replacement value</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	107 </param>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	108 <when value="--fail-on-non-computable" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	109 <when value="--skip-non-computable" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	110 <when value="--keep-non-computable" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	111 <when value="--non-computable-blank" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	112 <when value="--non-computable-default">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	113 <param name="default_value" type="text" label="Replacement value" help="Pick from suggestions or enter your own.">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	114 <option value="nan">nan (not a number)</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	115 <option value="inf">inf (infinity)</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	116 <option value="-inf">-inf (negative infinity)</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	117 <option value="NA">NA (not available)</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	118 <option value=".">.</option>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	119 </param>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	120 </when>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	121 </conditional>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	122 </section>
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	123 </inputs>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	124 <outputs>
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	125 <data name="out_file1" format_source="input" metadata_source="input"/>
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	126 </outputs>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	127 <tests>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	128 <test>
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	129 <param name="cond" value="float(c3-c2)"/>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	130 <param name="input" value="1.bed" ftype="bed" />
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	131 <output name="out_file1" file="column_maker_out1.interval"/>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	132 </test>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	133 <test>
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	134 <param name="cond" value="c4*1."/>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	135 <param name="input" value="1.interval" ftype="interval" />
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	136 <output name="out_file1" file="column_maker_out2.interval"/>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	137 </test>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	138 <test>
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	139 <param name="cond" value="c4*1."/>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	140 <param name="input" value="1.header.tsv" ftype="tabular" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	141 <param name="header_lines_select" value="yes" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	142 <param name="new_column_name" value="value1_again" />
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	143 <output name="out_file1" file="column_maker_out2.header.tsv"/>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	144 </test>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	145 <test>
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	146 <param name="cond" value="round(c4*1)"/>
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	147 <param name="input" value="1.interval"/>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	148 <output name="out_file1" file="column_maker_out3.interval"/>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	149 </test>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	150 <test>
8 227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e" devteam parents: 7 diff changeset	151 <!-- test that single column input works -->
227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e" devteam parents: 7 diff changeset	152 <param name="cond" value="c1/10"/>
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	153 <param name="input" value="1.tab" ftype="tabular" />
8 227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e" devteam parents: 7 diff changeset	154 <output name="out_file1" file="column_maker_out4.tab"/>
227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e" devteam parents: 7 diff changeset	155 </test>
227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e" devteam parents: 7 diff changeset	156 <test>
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	157 <param name="cond" value="float(.0000000000001)"/>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	158 <param name="input" value="1.bed"/>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	159 <output name="out_file1">
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	160 <assert_contents>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	161 <has_text text="CCDS10397" />
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	162 <has_text text="1e-13" />
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	163 </assert_contents>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	164 </output>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	165 </test>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	166 <test>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	167 <param name="cond" value="float(.0000000000001)"/>
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	168 <param name="input" value="1.bed" ftype="bed" />
7 e7c273e8d4d6 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187" devteam parents: 6 diff changeset	169 <param name="avoid_scientific_notation" value="true"/>
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	170 <output name="out_file1">
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	171 <assert_contents>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	172 <has_text text="CCDS10397" />
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	173 <has_text text=".0000000000001" />
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	174 <not_has_text text="1e-13" />
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	175 </assert_contents>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	176 </output>
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	177 </test>
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	178 <test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	179 <param name="input" value="1.tab" ftype="tabular" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	180 <repeat name="expressions">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	181 <param name="cond" value="c1/10" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	182 <conditional name="add_column">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	183 <param name="mode" value="R" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	184 <param name="pos" value="1" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	185 </conditional>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	186 </repeat>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	187 <repeat name="expressions">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	188 <param name="cond" value="round(c1*10)" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	189 <conditional name="add_column">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	190 <param name="mode" value="I" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	191 <param name="pos" value="1" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	192 </conditional>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	193 </repeat>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	194 <output name="out_file1" file="column_maker_out4.tab" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	195 </test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	196 <!-- Test list column type in input -->
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	197 <test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	198 <param name="input" value="bed12.bed" ftype="bed12" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	199 <!-- get largest blocksize from column 11 of bed12 and use it as
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	200 new score value -->
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	201 <param name="cond" value="max(map(int, c11))" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	202 <conditional name="add_column">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	203 <param name="mode" value="R" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	204 <param name="pos" value="5" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	205 </conditional>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	206 <output name="out_file1" file="bed12_modified.bed" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	207 </test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	208 <!-- Test error handling example from help section -->
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	209 <test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	210 <param name="input" value="short_line_test.tab" ftype="tabular" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	211 <param name="cond" value="c6" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	212 <conditional name="add_column">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	213 <param name="mode" value="R" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	214 <param name="pos" value="6" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	215 </conditional>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	216 <param name="fail_on_non_existent_columns" value="false" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	217 <param name="action" value="--non-computable-default" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	218 <param name="default_value" value="." />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	219 <output name="out_file1" file="short_line_test_out.tab" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	220 </test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	221 <!-- Test athletes BMI calculation in presence of NA values as in
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	222 https://training.galaxyproject.org/training-material/topics/introduction/tutorials/data-manipulation-olympics/tutorial.html#exercises-4
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	223 -->
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	224 <test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	225 <param name="input" value="olympics.tsv" ftype="tabular" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	226 <param name="header_lines_select" value="yes" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	227 <param name="new_column_name" value="BMI" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	228 <param name="cond" value="int(c8) / (int(c7) * int(c7)) * 10000" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	229 <param name="auto_col_types" value="false" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	230 <param name="action" value="--non-computable-default" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	231 <param name="default_value" value="NA" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	232 <output name="out_file1" file="olympics_bmi_out.tab" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	233 </test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	234 <!-- Test operation used by iwc SARS-CoV-2 consensus building WF that
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	235 turns a 3-column CHROM POS REF tabular dataset into a 3-column BED
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	236 dataset. -->
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	237 <test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	238 <param name="input" value="chrom_pos_ref.tab" ftype="tabular" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	239 <repeat name="expressions">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	240 <param name="cond" value="int(c2) - (len(c3) == 1)" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	241 <conditional name="add_column">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	242 <param name="mode" value="R" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	243 <param name="pos" value="2" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	244 </conditional>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	245 </repeat>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	246 <repeat name="expressions">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	247 <param name="cond" value="int(c2) + ((len(c3) - 1) or 1)" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	248 <conditional name="add_column">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	249 <param name="mode" value="R" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	250 <param name="pos" value="3" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	251 </conditional>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	252 </repeat>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	253 <output name="out_file1" file="bed_from_chrom_pos_ref.bed" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	254 </test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	255 <!-- Test failure on expression syntax errors -->
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	256 <test expect_failure="true">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	257 <param name="cond" value="c3- = c2"/>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	258 <param name="input" value="1.bed" ftype="bed" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	259 <assert_stderr>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	260 <has_text text="syntax error during parsing." />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	261 </assert_stderr>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	262 </test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	263 <!-- Test failure on expression NameErrors -->
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	264 <test expect_failure="true">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	265 <param name="cond" value="floatfloat(c3-c2)"/>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	266 <param name="input" value="1.bed" ftype="bed" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	267 <assert_stderr>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	268 <has_text text="name 'floatfloat' is not defined" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	269 </assert_stderr>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	270 </test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	271 <!-- Test failure on non-existent column ref -->
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	272 <test expect_failure="true">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	273 <param name="cond" value="c7 - c2"/>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	274 <param name="input" value="1.bed" ftype="bed" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	275 <assert_stderr>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	276 <has_text text="name 'c7' is not defined" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	277 </assert_stderr>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	278 </test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	279 <!-- Test failure on non-computable expression -->
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	280 <test expect_failure="true">
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	281 <param name="cond" value="c3 / 0"/>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	282 <param name="input" value="1.bed" ftype="bed" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	283 <assert_stderr>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	284 <has_text text="division by zero" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	285 </assert_stderr>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	286 </test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	287 <!-- Test keep-non-computable prevents failure -->
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	288 <test>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	289 <param name="cond" value="c3 / 0"/>
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	290 <param name="input" value="1.bed" ftype="bed" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	291 <param name="action" value="--keep-non-computable" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	292 <output name="out_file1" file="1.bed" />
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	293 </test>
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	294 </tests>
8 227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e" devteam parents: 7 diff changeset	295 <help><![CDATA[
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	296 .. class:: infomark
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	297
8 227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e" devteam parents: 7 diff changeset	298 TIP: If your data is not TAB delimited, use Text Manipulation->Convert
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	299
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	300 -----
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	301
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	302 What it does
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	303
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	304 This tool computes an expression on every row of a dataset and appends or inserts the result as a new column (field).
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	305
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	306 Several expressions can be specified and will be applied sequentially to each row.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	307
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	308 Expression rules
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	309
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	310 - Columns are referenced with c and a number. For example, c1 refers to the first column of a tab-delimited file
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	311
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	312 - The following built-in Python functions are available for use in expressions::
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	313
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	314 abs \| all \| any \| ascii \| bin \| bool \| chr \| ceil \| complex \| divmod
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	315
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	316 exp \| float \| floor \| format \| hex \| int \| len \| list \| log \| log10
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	317
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	318 list \| map \| max \| min \| oct \| ord \| pow \| range \| reversed
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	319
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	320 round \| set \| sorted \| sqrt \| str \| sum \| type
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	321
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	322 - In addition the numpy function ``format_float_positional`` is available to
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	323 control the formatting of floating point numbers.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	324
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	325 - Expressions can be chained, and the tool will keep track of newly added
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	326 columns while working through the chain. This means you can reference a column
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	327 that was created as the result of a previous expression in later ones.
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	328
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	329 -----
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	330
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	331 Simple examples
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	332
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	333 If this is your input::
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	334
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	335 chr1 151077881 151077918 2 200 -
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	336 chr1 151081985 151082078 3 500 +
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	337
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	338 computing "c4 * c5" will produce::
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	339
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	340 chr1 151077881 151077918 2 200 - 400
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	341 chr1 151081985 151082078 3 500 + 1500
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	342
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	343 You can also use this tool to evaluate expressions.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	344 For example, computing "c3 >= c2" for the input above will result in the following::
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	345
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	346 chr1 151077881 151077918 2 200 - True
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	347 chr1 151081985 151082078 3 500 + True
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	348
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	349 Similarly, computing "type(c2) == type(c3) will return::
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	350
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	351 chr1 151077881 151077918 2 200 - True
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	352 chr1 151081985 151082078 3 500 + True
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	353
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	354 -----
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	355
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	356 Error handling
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	357
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	358 The tool will always fail on syntax errors in and other unrecoverable parsing
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	359 errors with any of your expressions. For other problems, however, it offers
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	360 control over how they should be handled:
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	361
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	362 1. The default for "Autodetect column types" is "Yes", which means the tool
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	363 will evaluate each column value as the type that Galaxy assumes for the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	364 column. This default behavior will allow you to write simpler expressions.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	365 The arithmetic expression "c4 * c5" from the first simple example,
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	366 for instance, works only because Galaxy realizes that c4 and c5 are integer
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	367 columns. Occasionally, this autodetection can cause issues. A common
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	368 such situation are missing values in columns that Galaxy thinks are of
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	369 numeric type. If you're getting errors like "Failed to convert some of the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	370 columns in line #X ...", a solution might be to turn off column type
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	371 autodetection. The price you will have to pay for doing so is that now you
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	372 will have to handle type conversions yourself. In the first example you would
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	373 now have to use the epression: "int(c4) * int(c5)".
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	374
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	375 2. By default, if any expression references columns that are not existing before
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	376 that expression gets computed, the tool will fail, but you can uncheck the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	377 "Fail on references to non-existent columns" option. If you do so, the result
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	378 will depend on your choice for "If an expression cannot be computed for a row"
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	379 (see 3.)
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	380
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	381 3. The default for rows, for which an expression fails to compute is, again, to
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	382 fail the tool run, but you can also choose to:
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	383
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	384 - skip the row on output
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	385
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	386 This is a simple way to only keep lines conforming to an expected standard.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	387 It is also easy to mask problems with your expressions with this option so
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	388 take a look at the results and try to understand what gets skipped and for
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	389 what reasons (the stdout of the tool will contain information about both).
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	390
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	391 - keep the row unchanged
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	392
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	393 This can be a good solution if your input contains special separator lines
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	394 that don't follow the general tabular format of other lines and you would
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	395 like to keep those lines
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	396
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	397 - produce an empty column value for the row
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	398
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	399 This will use the empty string as a substitute for non-computable items.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	400 Different from the "keep the row unchanged option" the problematic line will
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	401 have a column added or changed. This option is a good choice for inputs
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	402 in which all rows have the same tabular layout where you want to make sure
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	403 that the same is true for the output, i.e. that all output lines still have
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	404 the same number of columns.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	405
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	406 - fill in a replacement value
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	407
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	408 This option is very similar to the previous one, but lets you control the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	409 replacement value.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	410
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	411 Example
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	412
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	413 In the following input::
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	414
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	415 chr1 151077881 151077918 2 200 -
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	416 chr1 151081985 151082078 3 500 +
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	417 chr1 151090031 151090938 4 700
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	418
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	419 the last line does not have a strand column. This violates the bed file format
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	420 specification, which says that unknown strand is to be encoded as ``.`` in the
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	421 strand column.
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	422
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	423 You can fix the file with the following tool run:
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	424
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	425 Add expression: `c6`
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	426
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	427 Mode of the operation: `Replace`
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	428
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	429 Use new column to replace column number: `6`
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	430
9 33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	431 Fail on references to non-existent columns: `No`
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	432
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	433 If an expression cannot be computed for a row: `Fill in a replacement value`
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	434
33b81f9ea109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit fe76077775aaca531f6a563fdfcbd73fbf1528e7 iuc parents: 8 diff changeset	435 Replacement value: `.`
8 227e82286a0e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit c623e4b9f6dd6ff4b88d9386f3b0a0cb497e0a0e" devteam parents: 7 diff changeset	436 ]]></help>
6 0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	437 <citations />
0aeda7a81b46 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236" devteam parents: 5 diff changeset	438 </tool>

Mercurial > repos > devteam > column_maker

annotate column_maker.xml @ 9:33b81f9ea109 draft