Mercurial > repos > bgruening > text_processing
annotate easyjoin.xml @ 2:616efa22d193 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
author | bgruening |
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date | Tue, 30 Jun 2015 17:47:23 -0400 |
parents | 43b1f073b693 |
children | 37e1eb05b1b4 |
rev | line source |
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0 | 1 <tool id="tp_easyjoin_tool" name="Join" version="@BASE_VERSION@.0"> |
2 <description>two files</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
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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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changeset
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6 <expand macro="requirements" /> |
0 | 7 <version_command>join --version | head -n 1</version_command> |
8 <command> | |
9 <![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
parents:
0
diff
changeset
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10 cp $__tool_directory__/sort-header ./ && |
0 | 11 chmod +x sort-header && |
1
43b1f073b693
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
bgruening
parents:
0
diff
changeset
|
12 perl $__tool_directory__/easyjoin |
0 | 13 $jointype |
14 -t ' ' | |
15 $header | |
16 -e '$empty_string_filler' | |
17 -o auto | |
18 $ignore_case | |
19 -1 '$column1' | |
20 -2 '$column2' | |
21 "$infile1" | |
22 "$infile2" | |
23 > '$output' | |
24 ]]> | |
25 </command> | |
26 <inputs> | |
27 <param name="infile1" format="tabular" type="data" label="1st file" /> | |
28 <param name="column1" label="Column to use from 1st file" type="data_column" data_ref="infile1" accept_default="true" /> | |
29 | |
30 <param name="infile2" format="txt" type="data" label="2nd File" /> | |
31 <param name="column2" label="Column to use from 2nd file" type="data_column" data_ref="infile2" accept_default="true" /> | |
32 | |
33 <param name="jointype" type="select" label="Output lines appearing in"> | |
34 <option value=" " selected="True">Both 1st & 2nd file.</option> | |
35 <option value="-v 1">1st but not in 2nd file. (-v 1)</option> | |
36 <option value="-v 2">2nd but not in 1st file. (-v 2)</option> | |
37 <option value="-a 1">Both 1st & 2nd file, plus unpairable lines from 1st file. (-a 1)</option> | |
38 <option value="-a 2">Both 1st & 2nd file, plus unpairable lines from 2st file. (-a 2)</option> | |
39 <option value="-a 1 -a 2">All lines [-a 1 -a 2]</option> | |
40 <option value="-v 1 -v 2">All unpairable lines [-v 1 -v 2]</option> | |
41 </param> | |
42 | |
43 <param name="header" type="boolean" checked="false" truevalue="--header" falsevalue="" | |
44 label="First line is a header line" help="Use if first line contains column headers. It will not be sorted." /> | |
45 <param name="ignore_case" type="boolean" checked="false" truevalue="-i" falsevalue="" | |
46 label="Ignore case" help="Sort and Join key column values regardless of upper/lower case letters." /> | |
47 <param name="empty_string_filler" type="text" size="20" value="0" label="Value to put in unpaired (empty) fields"> | |
48 <sanitizer> | |
49 <valid initial="string.printable"> | |
50 <remove value="'"/> | |
51 </valid> | |
52 </sanitizer> | |
53 </param> | |
54 </inputs> | |
55 <outputs> | |
56 <data name="output" format_source="infile1" metadata_source="infile1"/> | |
57 </outputs> | |
58 <tests> | |
59 <test> | |
60 <param name="infile1" value="easyjoin1.tabular" /> | |
61 <param name="column1" value="1" /> | |
62 <param name="infile2" value="easyjoin2.tabular" /> | |
63 <param name="column2" value="1" /> | |
64 <param name="header" value="True" /> | |
65 <param name="jointype" value="-a 1 -a 2" /> | |
66 <output name="output" file="easyjoin_result1.tabular" /> | |
67 </test> | |
68 </tests> | |
69 <help> | |
70 <![CDATA[ | |
71 **What it does** | |
72 | |
73 This tool joins two tabular files based on a common key column. | |
74 | |
75 ----- | |
76 | |
77 **Example** | |
78 | |
79 **First file**:: | |
80 | |
81 Fruit Color | |
82 Apple red | |
83 Banana yellow | |
84 Orange orange | |
85 Melon green | |
86 | |
87 **Second File**:: | |
88 | |
89 Fruit Price | |
90 Orange 7 | |
91 Avocado 8 | |
92 Apple 4 | |
93 Banana 3 | |
94 | |
95 **Joining** both files, using **key column 1** and a **header line**, will return:: | |
96 | |
97 Fruit Color Price | |
98 Apple red 4 | |
99 Avocado . 8 | |
100 Banana yellow 3 | |
101 Melon green . | |
102 Orange orange 7 | |
103 | |
104 .. class:: infomark | |
105 | |
106 * Input files need not be sorted. | |
107 * The header line (**Fruit Color Price**) was joined and kept as first line. | |
108 * Missing values ( Avocado's color, missing from the first file ) are replaced with a period character. | |
109 | |
110 @REFERENCES@ | |
111 ]]> | |
112 </help> | |
113 </tool> |