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comparison column_maker.xml @ 6:13b6f0007d9e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"
author devteam
date Mon, 25 Jan 2021 10:00:12 +0000
parents 9cd341095afd
children 427903d47026
comparison
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5:9cd341095afd 6:13b6f0007d9e
1 <tool id="Add_a_column1" name="Compute" version="1.4"> 1 <tool id="Add_a_column1" name="Compute" version="1.5">
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="3.8">python</requirement> 4 <requirement type="package" version="3.8">python</requirement>
5 <requirement type="package" version="4.4">sed</requirement>
6 <requirement type="package" version="1.19.1">numpy</requirement> 5 <requirement type="package" version="1.19.1">numpy</requirement>
7 </requirements> 6 </requirements>
8 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
9 #if $header_lines_conditional.header_lines_select == "yes": 8 ln -s '$input' data &&
10 (sed -n '1,1p' '$input' | sed "s|$|%${header_lines_conditional.header_new_column_name}|" | tr "%" "\t") > header &&
11 sed '1,1d' '$input' > data &&
12 #else:
13 touch header &&
14 ln -s '$input' data &&
15 #end if
16 9
17 ## inject colums and column_types metadata into inputs json 10 ## inject colums and column_types metadata into inputs json
18 #import json 11 #import json
19 #set inputs_dict = json.load(open($inputs)) 12 #set inputs_dict = json.load(open($inputs))
20 #set inputs_dict['columns'] = $input.metadata.columns 13 #set inputs_dict['columns'] = $input.metadata.columns
21 #set inputs_dict['column_types'] = $input.metadata.column_types 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
22 #set x = json.dump($inputs_dict, open($inputs, 'w')) 19 #set x = json.dump($inputs_dict, open($inputs, 'w'))
23 20
24 python '$__tool_directory__/column_maker.py' 21 python '$__tool_directory__/column_maker.py'
25 data column_maker_output 22 data '$out_file1'
26 --load_json '$inputs' 23 --load_json '$inputs'
27 && cat header column_maker_output > '$out_file1'
28 ]]></command> 24 ]]></command>
29 <configfiles> 25 <configfiles>
30 <inputs name="inputs"/> 26 <inputs name="inputs"/>
31 </configfiles> 27 </configfiles>
32 <inputs> 28 <inputs>
33 <param name="cond" type="text" value="c3-c2" label="Add expression"/> 29 <param name="cond" type="text" value="c3-c2" label="Add expression">
30 <sanitizer>
31 <valid initial="default">
32 <add value="&lt;" />
33 <add value="&gt;" />
34 <add value="&quot;" />
35 <add value="&apos;" />
36 </valid>
37 </sanitizer>
38 </param>
34 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/> 39 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>
35 <param name="round" type="select" label="Round result?"> 40 <param name="round" type="boolean" truevalue="yes" falsevalue="no" label="Round result?" />
36 <option value="no">NO</option> 41 <param name="avoid_scientific_notation" type="boolean" truevalue="yes" falsevalue="no"
37 <option value="yes">YES</option> 42 label="Avoid scientific notation"
38 </param> 43 help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers)." />
39 <conditional name="header_lines_conditional"> 44 <conditional name="header_lines_conditional">
40 <param name="header_lines_select" type="select" label="Skip a header line" help="# characters are already considered as comments and kept" > 45 <param name="header_lines_select" type="select"
41 <option value="no" >no</option> 46 label="Input has a header line with column names?"
42 <option value="yes" >yes</option> 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." >
48 <option value="no" >No</option>
49 <option value="yes" >Yes</option>
43 </param> 50 </param>
44 <when value="no"> 51 <when value="no">
45 </when> 52 </when>
46 <when value="yes"> 53 <when value="yes">
47 <param name="header_new_column_name" type="text" value="New Column" label="The new column name" /> 54 <param name="header_new_column_name" type="text" value="New Column" label="The new column name" />
48 </when> 55 </when>
49 </conditional> 56 </conditional>
50 <param name="avoid_scientific_notation" type="select" label="Avoid scientific notation" help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers).">
51 <option value="no">no</option>
52 <option value="yes">yes</option>
53 </param>
54 </inputs> 57 </inputs>
55 <outputs> 58 <outputs>
56 <data format_source="input" name="out_file1" metadata_source="input"/> 59 <data format_source="input" name="out_file1" metadata_source="input"/>
57 </outputs> 60 </outputs>
58 <tests> 61 <tests>
59 <test> 62 <test>
60 <param name="cond" value="c3-c2"/> 63 <param name="cond" value="c3-c2"/>
61 <param name="input" value="1.bed"/> 64 <param name="input" value="1.bed"/>
62 <param name="round" value="no"/> 65 <param name="round" value="false"/>
63 <output name="out_file1" file="column_maker_out1.interval"/> 66 <output name="out_file1" file="column_maker_out1.interval"/>
64 </test> 67 </test>
65 <test> 68 <test>
66 <param name="cond" value="c4*1"/> 69 <param name="cond" value="c4*1"/>
67 <param name="input" value="1.interval"/> 70 <param name="input" value="1.interval"/>
68 <param name="round" value="no"/> 71 <param name="round" value="false"/>
69 <output name="out_file1" file="column_maker_out2.interval"/> 72 <output name="out_file1" file="column_maker_out2.interval"/>
70 </test> 73 </test>
71 <test> 74 <test>
72 <param name="cond" value="c4*1"/> 75 <param name="cond" value="c4*1"/>
73 <param name="input" value="1.header.tsv"/> 76 <param name="input" value="1.header.tsv"/>
74 <param name="round" value="no"/> 77 <param name="round" value="false"/>
75 <conditional name="header_lines_conditional"> 78 <conditional name="header_lines_conditional">
76 <param name="header_lines_select" value="yes" /> 79 <param name="header_lines_select" value="yes" />
77 <param name="header_new_column_name" value="value1_again" /> 80 <param name="header_new_column_name" value="value1_again" />
78 </conditional> 81 </conditional>
79 <output name="out_file1" file="column_maker_out2.header.tsv"/> 82 <output name="out_file1" file="column_maker_out2.header.tsv"/>
80 </test> 83 </test>
81 <test> 84 <test>
82 <param name="cond" value="c4*1"/> 85 <param name="cond" value="c4*1"/>
83 <param name="input" value="1.interval"/> 86 <param name="input" value="1.interval"/>
84 <param name="round" value="yes"/> 87 <param name="round" value="true"/>
85 <output name="out_file1" file="column_maker_out3.interval"/> 88 <output name="out_file1" file="column_maker_out3.interval"/>
86 </test> 89 </test>
87 <test> 90 <test>
88 <param name="cond" value="float(.0000000000001)"/> 91 <param name="cond" value="float(.0000000000001)"/>
89 <param name="input" value="1.bed"/> 92 <param name="input" value="1.bed"/>
90 <param name="round" value="no"/> 93 <param name="round" value="false"/>
91 <output name="out_file1"> 94 <output name="out_file1">
92 <assert_contents> 95 <assert_contents>
93 <has_text text="CCDS10397" /> 96 <has_text text="CCDS10397" />
94 <has_text text="1e-13" /> 97 <has_text text="1e-13" />
95 </assert_contents> 98 </assert_contents>
96 </output> 99 </output>
97 </test> 100 </test>
98 <test> 101 <test>
99 <param name="cond" value="float(.0000000000001)"/> 102 <param name="cond" value="float(.0000000000001)"/>
100 <param name="input" value="1.bed"/> 103 <param name="input" value="1.bed"/>
101 <param name="round" value="no"/> 104 <param name="round" value="false"/>
102 <param name="avoid_scientific_notation" value="yes"/> 105 <param name="avoid_scientific_notation" value="true"/>
103 <output name="out_file1"> 106 <output name="out_file1">
104 <assert_contents> 107 <assert_contents>
105 <has_text text="CCDS10397" /> 108 <has_text text="CCDS10397" />
106 <has_text text=".0000000000001" /> 109 <has_text text=".0000000000001" />
107 <not_has_text text="1e-13" /> 110 <not_has_text text="1e-13" />