Mercurial > repos > iuc > obi_uniq
comparison obiuniq.xml @ 0:4c2b715a258a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
author | iuc |
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date | Wed, 12 Apr 2017 17:38:18 -0400 |
parents | |
children | e0655b546470 |
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-1:000000000000 | 0:4c2b715a258a |
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1 <tool id="obi_uniq" name="obiuniq" version="@WRAPPER_VERSION@"> | |
2 <macros> | |
3 <import>macros.xml</import> | |
4 </macros> | |
5 <expand macro="requirements"/> | |
6 <expand macro="stdio"/> | |
7 <command> | |
8 | |
9 <![CDATA[ | |
10 | |
11 obiuniq | |
12 #if str( $options_attribute) == "merge" | |
13 -m '$options_uniq' | |
14 #else | |
15 -c '$options_uniq' | |
16 #end if | |
17 ${mid} | |
18 ${prefix} | |
19 '$input' > '$output' | |
20 | |
21 ]]> | |
22 | |
23 </command> | |
24 | |
25 <inputs> | |
26 <param name="input" type="data" format="fasta,fastq" label="Input sequences file" /> | |
27 <param name="options_uniq" type="select" label="Attribute to merge" > | |
28 <expand macro="attributes"/> | |
29 </param> | |
30 <param name="options_attribute" type="select" label="Use specific option" > | |
31 <option value="merge" selected="true">merge</option> | |
32 <option value="category_attribute">category_attribute</option> | |
33 </param> | |
34 <param name="mid" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Add a merged attribute containing the list of sequence record ids merged within this group" /> | |
35 <param name="prefix" type="boolean" checked="false" truevalue="-p" falsevalue="" label="Dereplicate through a prefix matching" /> | |
36 </inputs> | |
37 <outputs> | |
38 <data format="fasta" name="output" label="output.fasta with ${tool.name} on ${on_string}" /> | |
39 </outputs> | |
40 | |
41 <tests> | |
42 <test> | |
43 <param name="input" value="output_ngsfilter_error_3.fastq" /> | |
44 <param name="options_uniq" value="sample" /> | |
45 <param name="options_attribute" value="merge" /> | |
46 <param name="mid" value="False" /> | |
47 <param name="prefix" value="False" /> | |
48 <output name="output" file="output_obiuniq.fasta" ftype="fasta"/> | |
49 </test> | |
50 <test> | |
51 <param name="input" value="output_ngsfilter_error_3.fastq" /> | |
52 <param name="options_uniq" value="family" /> | |
53 <param name="options_attribute" value="category_attribute" /> | |
54 <param name="mid" value="True" /> | |
55 <param name="prefix" value="True" /> | |
56 <output name="output" file="output_obiuniq_family.fasta" ftype="fasta"/> | |
57 </test> | |
58 | |
59 </tests> | |
60 <help><![CDATA[ | |
61 | |
62 .. class:: infomark | |
63 | |
64 **What it does** | |
65 | |
66 The obiuniq command is in some way analog to the standard Unix uniq -c command. | |
67 | |
68 Instead of working text line by text line as the standard Unix tool, the processing is done on sequence records. | |
69 | |
70 A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself. | |
71 | |
72 The obiuniq command groups together sequence records. Then, for each group, a sequence record is printed. | |
73 | |
74 A group is defined by the sequence and optionally by the values of a set of attributes specified with the -c option. | |
75 | |
76 As the identifier, the set of attributes (key=value) and the definition of the sequence records that are grouped together may be different, two options (-m and -i) allow refining how these parts of the records are reported. | |
77 | |
78 \* By default, only attributes with identical values within a group of sequence records are kept. | |
79 | |
80 \* A count attribute is set to the total number of sequence records for each group. | |
81 | |
82 \* For each attribute specified by the -m option, a new attribute whose key is prefixed by merged_ is created. These new attributes contain the number of times each value occurs within the group of sequence records. | |
83 | |
84 | |
85 @OBITOOLS_LINK@ | |
86 | |
87 | |
88 | |
89 ]]> | |
90 </help> | |
91 <expand macro="citation" /> | |
92 </tool> |