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comparison column_maker.xml @ 5:9cd341095afd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit a993d43d9d1702a6cf584683cf72527a3f999236"
author devteam
date Wed, 30 Dec 2020 00:50:15 +0000
parents 6e8d94597139
children 13b6f0007d9e
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4:6e8d94597139 5:9cd341095afd
1 <tool id="Add_a_column1" name="Compute" version="1.3.1"> 1 <tool id="Add_a_column1" name="Compute" version="1.4">
2 <description>an expression on every row</description> 2 <description>an expression on every row</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7.13">python</requirement> 4 <requirement type="package" version="3.8">python</requirement>
5 <requirement type="package" version="4.4">sed</requirement> 5 <requirement type="package" version="4.4">sed</requirement>
6 <requirement type="package" version="1.14">numpy</requirement> 6 <requirement type="package" version="1.19.1">numpy</requirement>
7 </requirements> 7 </requirements>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 #if $header_lines_conditional.header_lines_select == "yes": 9 #if $header_lines_conditional.header_lines_select == "yes":
10 (sed -n '1,1p' '$input' | sed "s|$|%${header_lines_conditional.header_new_column_name}|" | tr "%" "\t") > header && 10 (sed -n '1,1p' '$input' | sed "s|$|%${header_lines_conditional.header_new_column_name}|" | tr "%" "\t") > header &&
11 sed '1,1d' '$input' > data && 11 sed '1,1d' '$input' > data &&
12 #else: 12 #else:
13 touch header && 13 touch header &&
14 ln -s '$input' data && 14 ln -s '$input' data &&
15 #end if 15 #end if
16 16
17 ## inject colums and column_types metadata into inputs json
18 #import json
19 #set inputs_dict = json.load(open($inputs))
20 #set inputs_dict['columns'] = $input.metadata.columns
21 #set inputs_dict['column_types'] = $input.metadata.column_types
22 #set x = json.dump($inputs_dict, open($inputs, 'w'))
23
17 python '$__tool_directory__/column_maker.py' 24 python '$__tool_directory__/column_maker.py'
18 data column_maker_output 25 data column_maker_output
19 "$cond" 26 --load_json '$inputs'
20 $round 27 && cat header column_maker_output > '$out_file1'
21 ${input.metadata.columns}
22 "${input.metadata.column_types}"
23 $avoid_scientific_notation &&
24 cat header column_maker_output > '$out_file1'
25 ]]></command> 28 ]]></command>
29 <configfiles>
30 <inputs name="inputs"/>
31 </configfiles>
26 <inputs> 32 <inputs>
27 <param name="cond" type="text" value="c3-c2" label="Add expression"/> 33 <param name="cond" type="text" value="c3-c2" label="Add expression"/>
28 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/> 34 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>
29 <param name="round" type="select" label="Round result?"> 35 <param name="round" type="select" label="Round result?">
30 <option value="no">NO</option> 36 <option value="no">NO</option>