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comparison column_maker.xml @ 8:02026300aa45 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"
author iuc
date Tue, 09 Mar 2021 18:33:10 +0000
parents 427903d47026
children 6595517c2dd8
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7:427903d47026 8:02026300aa45
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.8">python</requirement> 4 <requirement type="package" version="3.8">python</requirement>
5 <requirement type="package" version="1.19.1">numpy</requirement> 5 <requirement type="package" version="1.19.1">numpy</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 ln -s '$input' data && 8 ## inject colums and column_types metadata into inputs json
9 #import json
10 #set inputs_dict = json.load(open($inputs))
11 #set inputs_dict['columns'] = $input.metadata.columns
12 #set inputs_dict['column_types'] = $input.metadata.column_types
13 ## flatten conditional
14 #if $header_lines_conditional.header_lines_select == "yes":
15 #set inputs_dict['header_new_column_name'] = str($header_lines_conditional.header_new_column_name)
16 #end if
17 #set x = json.dump($inputs_dict, open($inputs, 'w'))
9 18
10 ## inject colums and column_types metadata into inputs json 19 python '$__tool_directory__/column_maker.py'
11 #import json 20 '$input'
12 #set inputs_dict = json.load(open($inputs)) 21 '$out_file1'
13 #set inputs_dict['columns'] = $input.metadata.columns 22 --load_json '$inputs'
14 #set inputs_dict['column_types'] = $input.metadata.column_types
15 ## flatten conditional
16 #if $header_lines_conditional.header_lines_select == "yes":
17 #set inputs_dict['header_new_column_name'] = str($header_lines_conditional.header_new_column_name)
18 #end if
19 #set x = json.dump($inputs_dict, open($inputs, 'w'))
20
21 python '$__tool_directory__/column_maker.py'
22 data '$out_file1'
23 --load_json '$inputs'
24 ]]></command> 23 ]]></command>
25 <configfiles> 24 <configfiles>
26 <inputs name="inputs"/> 25 <inputs name="inputs"/>
27 </configfiles> 26 </configfiles>
28 <inputs> 27 <inputs>
34 <add value="&quot;" /> 33 <add value="&quot;" />
35 <add value="&apos;" /> 34 <add value="&apos;" />
36 </valid> 35 </valid>
37 </sanitizer> 36 </sanitizer>
38 </param> 37 </param>
39 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/> 38 <param name="input" type="data" format="tabular" label="as a new column to" help="Dataset missing? See TIP below"/>
40 <param name="round" type="boolean" truevalue="yes" falsevalue="no" label="Round result?" /> 39 <param name="round" type="boolean" truevalue="yes" falsevalue="no" label="Round result?" />
41 <param name="avoid_scientific_notation" type="boolean" truevalue="yes" falsevalue="no" 40 <param name="avoid_scientific_notation" type="boolean" truevalue="yes" falsevalue="no"
42 label="Avoid scientific notation" 41 label="Avoid scientific notation"
43 help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers)." /> 42 help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers)." />
44 <conditional name="header_lines_conditional"> 43 <conditional name="header_lines_conditional">
45 <param name="header_lines_select" type="select" 44 <param name="header_lines_select" type="select"
46 label="Input has a header line with column names?" 45 label="Input has a header line with column names?"
47 help="Select Yes to be able to specify a name for the new column and have it 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." > 46 help="Select Yes to be able to specify a name for the new column and have it 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." >
48 <option value="no" >No</option> 47 <option value="no">No</option>
49 <option value="yes" >Yes</option> 48 <option value="yes">Yes</option>
50 </param> 49 </param>
51 <when value="no"> 50 <when value="no" />
52 </when>
53 <when value="yes"> 51 <when value="yes">
54 <param name="header_new_column_name" type="text" value="New Column" label="The new column name" /> 52 <param name="header_new_column_name" type="text" value="New Column" label="The new column name" />
55 </when> 53 </when>
56 </conditional> 54 </conditional>
57 </inputs> 55 </inputs>
58 <outputs> 56 <outputs>
59 <data format_source="input" name="out_file1" metadata_source="input"/> 57 <data name="out_file1" format_source="input" metadata_source="input"/>
60 </outputs> 58 </outputs>
61 <tests> 59 <tests>
62 <test> 60 <test>
63 <param name="cond" value="c3-c2"/> 61 <param name="cond" value="c3-c2"/>
64 <param name="input" value="1.bed"/> 62 <param name="input" value="1.bed"/>
118 </assert_contents> 116 </assert_contents>
119 </output> 117 </output>
120 </test> 118 </test>
121 </tests> 119 </tests>
122 <help><![CDATA[ 120 <help><![CDATA[
123
124 .. class:: infomark 121 .. class:: infomark
125 122
126 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* 123 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
127 124
128 ----- 125 -----