annotate easyjoin.xml @ 21:86755160afbf draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit c2b1677d1c94433f777c2dc28ac8eec0a99cc6a7
author bgruening
date Fri, 16 Aug 2024 10:41:54 +0000
parents 12615d397df7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
bgruening
parents: 14
diff changeset
1 <tool id="tp_easyjoin_tool" name="Join" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
2 <description>two files</description>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
3 <macros>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
4 <import>macros.xml</import>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
5 </macros>
19
12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
bgruening
parents: 14
diff changeset
6 <expand macro="creator"/>
5
20344ce0c811 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
parents: 3
diff changeset
7 <expand macro="requirements">
19
12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
bgruening
parents: 14
diff changeset
8 <requirement type="package" version="5.32">perl</requirement>
5
20344ce0c811 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
bgruening
parents: 3
diff changeset
9 </expand>
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
10 <version_command>join --version | head -n 1</version_command>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
11 <command>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
12 <![CDATA[
19
12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
bgruening
parents: 14
diff changeset
13 cp '$__tool_directory__/sort-header' ./ &&
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
14 chmod +x sort-header &&
19
12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
bgruening
parents: 14
diff changeset
15 perl '$__tool_directory__/easyjoin'
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
16 $jointype
14
fb4ff3c42cd3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 09b22cceacb34dd4c6c1b42890f93232df128208"
bgruening
parents: 7
diff changeset
17 -t $'\t'
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
18 $header
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
19 -e '$empty_string_filler'
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
20 -o auto
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
21 $ignore_case
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
22 -1 '$column1'
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
23 -2 '$column2'
19
12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
bgruening
parents: 14
diff changeset
24 '$infile1'
12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
bgruening
parents: 14
diff changeset
25 '$infile2'
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
26 > '$output'
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
27 ]]>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
28 </command>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
29 <inputs>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
30 <param name="infile1" format="tabular" type="data" label="1st file" />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
31 <param name="column1" label="Column to use from 1st file" type="data_column" data_ref="infile1" accept_default="true" />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
32
14
fb4ff3c42cd3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 09b22cceacb34dd4c6c1b42890f93232df128208"
bgruening
parents: 7
diff changeset
33 <param name="infile2" format="tabular" type="data" label="2nd File" />
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
34 <param name="column2" label="Column to use from 2nd file" type="data_column" data_ref="infile2" accept_default="true" />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
35
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
36 <param name="jointype" type="select" label="Output lines appearing in">
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
37 <option value=" " selected="True">Both 1st &amp; 2nd file.</option>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
38 <option value="-v 1">1st but not in 2nd file. (-v 1)</option>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
39 <option value="-v 2">2nd but not in 1st file. (-v 2)</option>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
40 <option value="-a 1">Both 1st &amp; 2nd file, plus unpairable lines from 1st file. (-a 1)</option>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
41 <option value="-a 2">Both 1st &amp; 2nd file, plus unpairable lines from 2st file. (-a 2)</option>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
42 <option value="-a 1 -a 2">All lines [-a 1 -a 2]</option>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
43 <option value="-v 1 -v 2">All unpairable lines [-v 1 -v 2]</option>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
44 </param>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
45
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
46 <param name="header" type="boolean" checked="false" truevalue="--header" falsevalue=""
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
47 label="First line is a header line" help="Use if first line contains column headers. It will not be sorted." />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
48 <param name="ignore_case" type="boolean" checked="false" truevalue="-i" falsevalue=""
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
49 label="Ignore case" help="Sort and Join key column values regardless of upper/lower case letters." />
3
37e1eb05b1b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents: 1
diff changeset
50 <param name="empty_string_filler" type="text" value="0" label="Value to put in unpaired (empty) fields">
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
51 <sanitizer>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
52 <valid initial="string.printable">
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
53 <remove value="&apos;"/>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
54 </valid>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
55 </sanitizer>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
56 </param>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
57 </inputs>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
58 <outputs>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
59 <data name="output" format_source="infile1" metadata_source="infile1"/>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
60 </outputs>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
61 <tests>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
62 <test>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
63 <param name="infile1" value="easyjoin1.tabular" />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
64 <param name="column1" value="1" />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
65 <param name="infile2" value="easyjoin2.tabular" />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
66 <param name="column2" value="1" />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
67 <param name="header" value="True" />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
68 <param name="jointype" value="-a 1 -a 2" />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
69 <output name="output" file="easyjoin_result1.tabular" />
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
70 </test>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
71 </tests>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
72 <help>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
73 <![CDATA[
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
74 **What it does**
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
75
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
76 This tool joins two tabular files based on a common key column.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
77
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
78 -----
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
79
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
80 **Example**
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
81
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
82 **First file**::
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
83
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
84 Fruit Color
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
85 Apple red
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
86 Banana yellow
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
87 Orange orange
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
88 Melon green
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
89
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
90 **Second File**::
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
91
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
92 Fruit Price
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
93 Orange 7
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
94 Avocado 8
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
95 Apple 4
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
96 Banana 3
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
97
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
98 **Joining** both files, using **key column 1** and a **header line**, will return::
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
99
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
100 Fruit Color Price
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
101 Apple red 4
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
102 Avocado . 8
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
103 Banana yellow 3
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
104 Melon green .
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
105 Orange orange 7
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
106
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
107 .. class:: infomark
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
108
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
109 * Input files need not be sorted.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
110 * The header line (**Fruit Color Price**) was joined and kept as first line.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
111 * Missing values ( Avocado's color, missing from the first file ) are replaced with a period character.
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
112
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
113 ]]>
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
114 </help>
6
60edf2f8c28f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
bgruening
parents: 5
diff changeset
115 <expand macro="citations" />
0
5314e5d6f040 Imported from capsule None
bgruening
parents:
diff changeset
116 </tool>