Mercurial > repos > bgruening > text_processing
annotate easyjoin.xml @ 16:ddf54b12c295 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit ded469a802a0496c9a6a2daee7b9505bd8698802-dirty"
author | bgruening |
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date | Tue, 06 Oct 2020 09:47:04 +0000 |
parents | fb4ff3c42cd3 |
children | 12615d397df7 |
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fb4ff3c42cd3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 09b22cceacb34dd4c6c1b42890f93232df128208"
bgruening
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1 <tool id="tp_easyjoin_tool" name="Join" version="@BASE_VERSION@.2"> |
0 | 2 <description>two files</description> |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
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20344ce0c811
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
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6 <expand macro="requirements"> |
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01ca80da2266
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
bgruening
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7 <requirement type="package" version="5.22.0.1">perl</requirement> |
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20344ce0c811
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
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8 </expand> |
0 | 9 <version_command>join --version | head -n 1</version_command> |
10 <command> | |
11 <![CDATA[ | |
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43b1f073b693
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
bgruening
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12 cp $__tool_directory__/sort-header ./ && |
0 | 13 chmod +x sort-header && |
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43b1f073b693
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
bgruening
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14 perl $__tool_directory__/easyjoin |
0 | 15 $jointype |
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fb4ff3c42cd3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 09b22cceacb34dd4c6c1b42890f93232df128208"
bgruening
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16 -t $'\t' |
0 | 17 $header |
18 -e '$empty_string_filler' | |
19 -o auto | |
20 $ignore_case | |
21 -1 '$column1' | |
22 -2 '$column2' | |
23 "$infile1" | |
24 "$infile2" | |
25 > '$output' | |
26 ]]> | |
27 </command> | |
28 <inputs> | |
29 <param name="infile1" format="tabular" type="data" label="1st file" /> | |
30 <param name="column1" label="Column to use from 1st file" type="data_column" data_ref="infile1" accept_default="true" /> | |
31 | |
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fb4ff3c42cd3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 09b22cceacb34dd4c6c1b42890f93232df128208"
bgruening
parents:
7
diff
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32 <param name="infile2" format="tabular" type="data" label="2nd File" /> |
0 | 33 <param name="column2" label="Column to use from 2nd file" type="data_column" data_ref="infile2" accept_default="true" /> |
34 | |
35 <param name="jointype" type="select" label="Output lines appearing in"> | |
36 <option value=" " selected="True">Both 1st & 2nd file.</option> | |
37 <option value="-v 1">1st but not in 2nd file. (-v 1)</option> | |
38 <option value="-v 2">2nd but not in 1st file. (-v 2)</option> | |
39 <option value="-a 1">Both 1st & 2nd file, plus unpairable lines from 1st file. (-a 1)</option> | |
40 <option value="-a 2">Both 1st & 2nd file, plus unpairable lines from 2st file. (-a 2)</option> | |
41 <option value="-a 1 -a 2">All lines [-a 1 -a 2]</option> | |
42 <option value="-v 1 -v 2">All unpairable lines [-v 1 -v 2]</option> | |
43 </param> | |
44 | |
45 <param name="header" type="boolean" checked="false" truevalue="--header" falsevalue="" | |
46 label="First line is a header line" help="Use if first line contains column headers. It will not be sorted." /> | |
47 <param name="ignore_case" type="boolean" checked="false" truevalue="-i" falsevalue="" | |
48 label="Ignore case" help="Sort and Join key column values regardless of upper/lower case letters." /> | |
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37e1eb05b1b4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
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49 <param name="empty_string_filler" type="text" value="0" label="Value to put in unpaired (empty) fields"> |
0 | 50 <sanitizer> |
51 <valid initial="string.printable"> | |
52 <remove value="'"/> | |
53 </valid> | |
54 </sanitizer> | |
55 </param> | |
56 </inputs> | |
57 <outputs> | |
58 <data name="output" format_source="infile1" metadata_source="infile1"/> | |
59 </outputs> | |
60 <tests> | |
61 <test> | |
62 <param name="infile1" value="easyjoin1.tabular" /> | |
63 <param name="column1" value="1" /> | |
64 <param name="infile2" value="easyjoin2.tabular" /> | |
65 <param name="column2" value="1" /> | |
66 <param name="header" value="True" /> | |
67 <param name="jointype" value="-a 1 -a 2" /> | |
68 <output name="output" file="easyjoin_result1.tabular" /> | |
69 </test> | |
70 </tests> | |
71 <help> | |
72 <![CDATA[ | |
73 **What it does** | |
74 | |
75 This tool joins two tabular files based on a common key column. | |
76 | |
77 ----- | |
78 | |
79 **Example** | |
80 | |
81 **First file**:: | |
82 | |
83 Fruit Color | |
84 Apple red | |
85 Banana yellow | |
86 Orange orange | |
87 Melon green | |
88 | |
89 **Second File**:: | |
90 | |
91 Fruit Price | |
92 Orange 7 | |
93 Avocado 8 | |
94 Apple 4 | |
95 Banana 3 | |
96 | |
97 **Joining** both files, using **key column 1** and a **header line**, will return:: | |
98 | |
99 Fruit Color Price | |
100 Apple red 4 | |
101 Avocado . 8 | |
102 Banana yellow 3 | |
103 Melon green . | |
104 Orange orange 7 | |
105 | |
106 .. class:: infomark | |
107 | |
108 * Input files need not be sorted. | |
109 * The header line (**Fruit Color Price**) was joined and kept as first line. | |
110 * Missing values ( Avocado's color, missing from the first file ) are replaced with a period character. | |
111 | |
112 @REFERENCES@ | |
113 ]]> | |
114 </help> | |
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60edf2f8c28f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
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115 <expand macro="citations" /> |
0 | 116 </tool> |