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comparison column_maker.xml @ 3:35937a6b04fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit f6e96ffa420035051ea4632596dfd171074aa66d
author devteam
date Thu, 25 Oct 2018 17:31:05 -0400
parents 292c605c2dc7
children 3335c0d583d8
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2:292c605c2dc7 3:35937a6b04fb
1 <tool id="Add_a_column1" name="Compute" version="1.1.0"> 1 <tool id="Add_a_column1" name="Compute" version="1.2.0">
2 <description>an expression on every row</description> 2 <description>an expression on every row</description>
3 <command interpreter="python"> 3 <requirements>
4 column_maker.py $input $out_file1 "$cond" $round ${input.metadata.columns} "${input.metadata.column_types}" 4 <requirement type="package" version="2.7.13">python</requirement>
5 </command> 5 <requirement type="package" version="4.4">sed</requirement>
6 <inputs> 6 </requirements>
7 <param name="cond" type="text" value="c3-c2" label="Add expression"/> 7 <command detect_errors="aggressive"><![CDATA[
8 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/> 8 #if $header_lines_conditional.header_lines_select == "yes":
9 <param name="round" type="select" label="Round result?"> 9 (sed -n '1,1p' '$input' | sed "s|$|%${header_lines_conditional.header_new_column_name}|" | tr "%" "\t") > header &&
10 <option value="no">NO</option> 10 sed '1,1d' '$input' > data &&
11 <option value="yes">YES</option> 11 #else:
12 </param> 12 touch header &&
13 </inputs> 13 ln -s '$input' data &&
14 <outputs> 14 #end if
15 <data format="input" name="out_file1" metadata_source="input"/> 15
16 </outputs> 16 python '$__tool_directory__/column_maker.py'
17 <tests> 17 data column_maker_output
18 <test> 18 "$cond"
19 <param name="cond" value="c3-c2"/> 19 $round
20 <param name="input" value="1.bed"/> 20 ${input.metadata.columns}
21 <param name="round" value="no"/> 21 "${input.metadata.column_types}" &&
22 <output name="out_file1" file="column_maker_out1.interval"/> 22 cat header column_maker_output > '$out_file1'
23 </test> 23 ]]></command>
24 <test> 24 <inputs>
25 <param name="cond" value="c4*1"/> 25 <param name="cond" type="text" value="c3-c2" label="Add expression"/>
26 <param name="input" value="1.interval"/> 26 <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>
27 <param name="round" value="no"/> 27 <param name="round" type="select" label="Round result?">
28 <output name="out_file1" file="column_maker_out2.interval"/> 28 <option value="no">NO</option>
29 </test> 29 <option value="yes">YES</option>
30 <test> 30 </param>
31 <param name="cond" value="c4*1"/> 31 <conditional name="header_lines_conditional">
32 <param name="input" value="1.interval"/> 32 <param name="header_lines_select" type="select" label="Skip a header line" help="# characters are already considered as comments and kept" >
33 <param name="round" value="yes"/> 33 <option value="no" >no</option>
34 <output name="out_file1" file="column_maker_out3.interval"/> 34 <option value="yes" >yes</option>
35 </test> 35 </param>
36 </tests> 36 <when value="no">
37 <help> 37 </when>
38 <when value="yes">
39 <param name="header_new_column_name" type="text" value="New Column" label="The new column name" />
40 </when>
41 </conditional>
42 </inputs>
43 <outputs>
44 <data format_source="input" name="out_file1" metadata_source="input"/>
45 </outputs>
46 <tests>
47 <test>
48 <param name="cond" value="c3-c2"/>
49 <param name="input" value="1.bed"/>
50 <param name="round" value="no"/>
51 <output name="out_file1" file="column_maker_out1.interval"/>
52 </test>
53 <test>
54 <param name="cond" value="c4*1"/>
55 <param name="input" value="1.interval"/>
56 <param name="round" value="no"/>
57 <output name="out_file1" file="column_maker_out2.interval"/>
58 </test>
59 <test>
60 <param name="cond" value="c4*1"/>
61 <param name="input" value="1.header.tsv"/>
62 <param name="round" value="no"/>
63 <conditional name="header_lines_conditional">
64 <param name="header_lines_select" value="yes" />
65 <param name="header_new_column_name" value="value1_again" />
66 </conditional>
67 <output name="out_file1" file="column_maker_out2.header.tsv"/>
68 </test>
69 <test>
70 <param name="cond" value="c4*1"/>
71 <param name="input" value="1.interval"/>
72 <param name="round" value="yes"/>
73 <output name="out_file1" file="column_maker_out3.interval"/>
74 </test>
75 </tests>
76 <help>
38 77
39 .. class:: infomark 78 .. class:: infomark
40 79
41 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert* 80 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
42 81
61 100
62 computing "c4*c5" will produce:: 101 computing "c4*c5" will produce::
63 102
64 chr1 151077881 151077918 2 200 - 400.0 103 chr1 151077881 151077918 2 200 - 400.0
65 chr1 151081985 151082078 3 500 + 1500.0 104 chr1 151081985 151082078 3 500 + 1500.0
66 105
67 if, at the same time, "Round result?" is set to **YES** results will look like this:: 106 if, at the same time, "Round result?" is set to **YES** results will look like this::
68 107
69 chr1 151077881 151077918 2 200 - 400 108 chr1 151077881 151077918 2 200 - 400
70 chr1 151081985 151082078 3 500 + 1500 109 chr1 151081985 151082078 3 500 + 1500
71 110
88 127
89 max | min | oct | ord | pow | range | reversed 128 max | min | oct | ord | pow | range | reversed
90 129
91 round | sorted | sqrt | str | sum | type | unichr | unicode | 130 round | sorted | sqrt | str | sum | type | unichr | unicode |
92 131
93 </help> 132 </help>
133 <citations />
94 </tool> 134 </tool>