Mercurial > repos > iuc > obi_uniq

annotate obiuniq.xml @ 4:d4bea99366f9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:16:55 +0000
parents ec215ed98831
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
1 <tool id="obi_uniq" name="obiuniq" version="@TOOL_VERSION@" profile="@PROFILE@">
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
2 <macros>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
3 <import>macros.xml</import>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
4 </macros>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
5 <expand macro="bio_tools"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
6 <expand macro="requirements"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
7 <expand macro="stdio"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
8 <command><![CDATA[
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
9 @GUNZIP_INPUT@
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
10
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
11 obiuniq
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
12 --without-progress-bar
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
13 #if str( $options_attribute) == "merge"
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
14 -m '$options_uniq'
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
15 #else
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
16 -c '$options_uniq'
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
17 #end if
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
18 ${mid}
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
19 ${prefix}
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
20 @INPUT_FORMAT@
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
21 input
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
22 @GZIP_OUTPUT@
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
23 > '$output'
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
24 @GENERATE_GALAXY_JSON@
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
25 ]]></command>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
26 <inputs>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
27 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
28 <param name="options_uniq" type="select" label="Attribute to merge">
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
29 <expand macro="attributes"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
30 </param>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
31 <param name="options_attribute" type="select" label="Use specific option">
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
32 <option value="merge" selected="true">merge</option>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
33 <option value="category_attribute">category_attribute</option>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
34 </param>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
35 <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"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
36 <param name="prefix" type="boolean" checked="false" truevalue="-p" falsevalue="" label="Dereplicate through a prefix matching"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
37 <expand macro="input_format_options_macro"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
38 </inputs>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
39 <outputs>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
40 <data format="auto" name="output"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
41 </outputs>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
42 <tests>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
43 <test expect_num_outputs="1">
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
44 <param name="input" value="output_ngsfilter_error_3.fastq" ftype="fastqsanger"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
45 <param name="options_uniq" value="sample"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
46 <param name="options_attribute" value="merge"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
47 <param name="mid" value="False"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
48 <param name="prefix" value="False"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
49 <output name="output" file="output_obiuniq.fasta" ftype="fasta"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
50 </test>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
51 <test expect_num_outputs="1">
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
52 <param name="input" value="output_ngsfilter_error_3.fastq.gz" ftype="fastqsanger.gz"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
53 <param name="options_uniq" value="family"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
54 <param name="options_attribute" value="category_attribute"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
55 <param name="mid" value="True"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
56 <param name="prefix" value="True"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
57 <output name="output" file="output_obiuniq_family.fasta.gz" ftype="fasta.gz" decompress="true"/>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
58 </test>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
59 </tests>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
60
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
61 <help><![CDATA[
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
62
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
63 .. class:: infomark
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
64
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
65 **What it does**
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
66
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
67 The obiuniq command is in some way analog to the standard Unix uniq -c command.
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
68
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
69 Instead of working text line by text line as the standard Unix tool, the processing is done on sequence records.
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
70
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
71 A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself.
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
72
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
73 The obiuniq command groups together sequence records. Then, for each group, a sequence record is printed.
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
74
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
75 A group is defined by the sequence and optionally by the values of a set of attributes specified with the -c option.
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
76
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
77 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.
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
78
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
79 \* By default, only attributes with identical values within a group of sequence records are kept.
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
80
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
81 \* A count attribute is set to the total number of sequence records for each group.
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
82
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
83 \* 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.
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
84
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
85
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
86 @OBITOOLS_LINK@
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
87 ]]>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
88
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
89 </help>
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
90 <expand macro="citation" />
d4bea99366f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
iuc
parents: 3
diff changeset
91 </tool>