Mercurial > repos > iuc > obi_uniq

comparison obiuniq.xml @ 3:ec215ed98831 draft

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 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
author iuc
date Mon, 10 May 2021 19:34:29 +0000
parents e0655b546470
children d4bea99366f9
comparison
equal deleted inserted replaced
2:c0f7b58b4ce4 3:ec215ed98831
1 <tool id="obi_uniq" name="obiuniq" version="@TOOL_VERSION@"> 1 <tool id="obi_uniq" name="obiuniq" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <macros> 2 <macros>
3 <import>macros.xml</import> 3 <import>macros.xml</import>
4 </macros> 4 </macros>
5 <expand macro="requirements"/> 5 <expand macro="requirements"/>
6 <expand macro="stdio"/> 6 <expand macro="stdio"/>
7 <command> 7 <command><![CDATA[
8 8 @GUNZIP_INPUT@
9 <![CDATA[
10 9
11 obiuniq 10 obiuniq
11 --without-progress-bar
12 #if str( $options_attribute) == "merge" 12 #if str( $options_attribute) == "merge"
13 -m '$options_uniq' 13 -m '$options_uniq'
14 #else 14 #else
15 -c '$options_uniq' 15 -c '$options_uniq'
16 #end if 16 #end if
17 ${mid} 17 ${mid}
18 ${prefix} 18 ${prefix}
19 '$input' > '$output' 19 @INPUT_FORMAT@
20 input
21 @GZIP_OUTPUT@
22 > '$output'
23 @GENERATE_GALAXY_JSON@
24 ]]></command>
25 <inputs>
26 <param name="input" type="data" format="@INPUT_FORMATS@" 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 <expand macro="input_format_options_macro"/>
37 </inputs>
38 <outputs>
39 <data format="auto" name="output"/>
40 </outputs>
41 <tests>
42 <test>
43 <param name="input" value="output_ngsfilter_error_3.fastq" ftype="fastqsanger"/>
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.gz" ftype="fastqsanger.gz"/>
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.gz" ftype="fasta.gz" decompress="true"/>
57 </test>
58 </tests>
59 <help><![CDATA[
60 .. class:: infomark
20 61
21 ]]> 62 **What it does**
22 63
23 </command> 64 The obiuniq command is in some way analog to the standard Unix uniq -c command.
24 65
25 <inputs> 66 Instead of working text line by text line as the standard Unix tool, the processing is done on sequence records.
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 67
41 <tests> 68 A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself.
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 69
59 </tests> 70 The obiuniq command groups together sequence records. Then, for each group, a sequence record is printed.
60 <help><![CDATA[
61 71
62 .. class:: infomark 72 A group is defined by the sequence and optionally by the values of a set of attributes specified with the -c option.
63 73
64 **What it does** 74 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.
65 75
66 The obiuniq command is in some way analog to the standard Unix uniq -c command. 76 \* By default, only attributes with identical values within a group of sequence records are kept.
67 77
68 Instead of working text line by text line as the standard Unix tool, the processing is done on sequence records. 78 \* A count attribute is set to the total number of sequence records for each group.
69 79
70 A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself. 80 \* 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.
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 81
84 82
85 @OBITOOLS_LINK@ 83 @OBITOOLS_LINK@
86 84 ]]></help>
87 85 <expand macro="citation" />
88
89 ]]>
90 </help>
91 <expand macro="citation" />
92 </tool> 86 </tool>