Mercurial > repos > bgruening > text_processing
annotate sorted_uniq.xml @ 6:60edf2f8c28f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author | bgruening |
---|---|
date | Sat, 06 May 2017 13:09:05 -0400 |
parents | 20344ce0c811 |
children | 74a8bef53a00 |
rev | line source |
---|---|
0 | 1 <tool id="tp_uniq_tool" name="Unique lines" version="@BASE_VERSION@.0"> |
2 <description>assuming sorted input file</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"> | |
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 <requirement type="package" version="4.2.3.dev0">sed</requirement> |
0 | 8 </expand> |
9 <version_command>uniq --version | head -n 1</version_command> | |
10 <command> | |
11 <![CDATA[ | |
12 uniq | |
13 #if $skipfields: | |
14 -f $skipfields | |
15 #end if | |
16 $ignorecase | |
17 | |
18 #if $grouping.grouping_select == 'yes': | |
19 --group=$grouping.group | |
20 #else: | |
21 $grouping.count | |
22 $grouping.repeated | |
23 $grouping.uniqueonly | |
24 #end if | |
25 | |
26 "$infile" | |
27 | |
28 #if $grouping.grouping_select == 'no' and $grouping.count: | |
29 ## count will print the count with spaces in front of the line and | |
30 ## with a space (not a tab) after the number, we need to cahnge that | |
31 | sed -e 's/ *//' -e 's/ /\t/' | |
32 #end if | |
33 > "$outfile" | |
34 ]]> | |
35 </command> | |
36 <inputs> | |
37 <param name="infile" format="tabular" type="data" | |
38 label="File to scan for unique values" help="Make sure you have sorted this file" /> | |
39 | |
40 <conditional name="grouping"> | |
41 <param name="grouping_select" type="select" label="Do you want to group each unique group?"> | |
42 <option value="no">No</option> | |
43 <option value="yes">Yes</option> | |
44 </param> | |
45 <when value="no"> | |
46 <param name="count" type="boolean" truevalue="-c" falsevalue="" | |
47 label="Counting number of occurrences" help="Prefix lines by the number of occurrences. (-c)" /> | |
48 <param name="repeated" type="boolean" truevalue="-d" falsevalue="" | |
49 label="Only print duplicate lines" help="(-d)"/> | |
50 <param name="uniqueonly" type="boolean" checked="True" truevalue="-u" falsevalue="" | |
51 label="Only print unique lines" help="(-u)" /> | |
52 </when> | |
53 <when value="yes"> | |
54 <param name="group" type="select" | |
55 label="Output all lines, and delimit each unique group" help="(--group)"> | |
56 <option value="">No grouping at all</option> | |
57 <option value="separate">Separate unique groups with a single delimiter</option> | |
58 <option value="prepend">Output a delimiter before each group of unique items</option> | |
59 <option value="append">Output a delimiter after each group of unique items</option> | |
60 <option value="both">Output a delimiter around each group of unique items</option> | |
61 </param> | |
62 </when> | |
63 </conditional> | |
64 | |
65 <param name="ignorecase" type="boolean" truevalue="-i" falsevalue="" | |
66 label="Ignore differences in case when comparing" help="(-i)"/> | |
3
37e1eb05b1b4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
bgruening
parents:
0
diff
changeset
|
67 <param name="skipfields" type="integer" value="0" |
0 | 68 label="Avoid comparing the first N fields" help="Use zero to start from the first field. (-f)" /> |
69 </inputs> | |
70 <outputs> | |
71 <data name="outfile" format_source="infile" metadata_source="infile"/> | |
72 </outputs> | |
73 <tests> | |
74 <test> | |
75 <param name="infile" value="sorted_uniq1.tabular" /> | |
76 <param name="grouping_select" value="no"/> | |
77 <param name="count" value="True"/> | |
78 <param name="ignorecase" value="True"/> | |
79 <param name="uniqueonly" value="True"/> | |
80 <output name="outfile" file="sorted_uniq_results1.tabular" /> | |
81 </test> | |
82 <test> | |
83 <param name="infile" value="sorted_uniq1.tabular" /> | |
84 <param name="ignorecase" value="True"/> | |
85 <param name="grouping_select" value="yes"/> | |
86 <param name="group" value="separate"/> | |
87 <output name="outfile" file="sorted_uniq_results2.tabular" /> | |
88 </test> | |
89 </tests> | |
90 <help> | |
91 <![CDATA[ | |
92 This tool takes a sorted file and look for lines that are unique. | |
93 | |
94 .. class:: warningmark | |
95 | |
96 Please make sure your file is sorted, or else this tool will give you an erroneous output. | |
97 | |
98 .. class:: infomark | |
99 | |
100 You can sort your file using either the "Sort" tool in "Filter and Sort", or the "Sort" tool in "Unix Tools". | |
101 | |
102 @REFERENCES@ | |
103 ]]> | |
104 </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
|
105 <expand macro="citations" /> |
0 | 106 </tool> |