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comparison obiuniq.xml @ 4:d4bea99366f9 draft default tip

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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
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3:ec215ed98831 4:d4bea99366f9
1 <tool id="obi_uniq" name="obiuniq" version="@TOOL_VERSION@" profile="@PROFILE@"> 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="bio_tools"/>
5 <expand macro="requirements"/> 6 <expand macro="requirements"/>
6 <expand macro="stdio"/> 7 <expand macro="stdio"/>
7 <command><![CDATA[ 8 <command><![CDATA[
8 @GUNZIP_INPUT@ 9 @GUNZIP_INPUT@
9 10
21 @GZIP_OUTPUT@ 22 @GZIP_OUTPUT@
22 > '$output' 23 > '$output'
23 @GENERATE_GALAXY_JSON@ 24 @GENERATE_GALAXY_JSON@
24 ]]></command> 25 ]]></command>
25 <inputs> 26 <inputs>
26 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" /> 27 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/>
27 <param name="options_uniq" type="select" label="Attribute to merge" > 28 <param name="options_uniq" type="select" label="Attribute to merge">
28 <expand macro="attributes"/> 29 <expand macro="attributes"/>
29 </param> 30 </param>
30 <param name="options_attribute" type="select" label="Use specific option" > 31 <param name="options_attribute" type="select" label="Use specific option">
31 <option value="merge" selected="true">merge</option> 32 <option value="merge" selected="true">merge</option>
32 <option value="category_attribute">category_attribute</option> 33 <option value="category_attribute">category_attribute</option>
33 </param> 34 </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="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 <param name="prefix" type="boolean" checked="false" truevalue="-p" falsevalue="" label="Dereplicate through a prefix matching"/>
36 <expand macro="input_format_options_macro"/> 37 <expand macro="input_format_options_macro"/>
37 </inputs> 38 </inputs>
38 <outputs> 39 <outputs>
39 <data format="auto" name="output"/> 40 <data format="auto" name="output"/>
40 </outputs> 41 </outputs>
41 <tests> 42 <tests>
42 <test> 43 <test expect_num_outputs="1">
43 <param name="input" value="output_ngsfilter_error_3.fastq" ftype="fastqsanger"/> 44 <param name="input" value="output_ngsfilter_error_3.fastq" ftype="fastqsanger"/>
44 <param name="options_uniq" value="sample" /> 45 <param name="options_uniq" value="sample"/>
45 <param name="options_attribute" value="merge" /> 46 <param name="options_attribute" value="merge"/>
46 <param name="mid" value="False" /> 47 <param name="mid" value="False"/>
47 <param name="prefix" value="False" /> 48 <param name="prefix" value="False"/>
48 <output name="output" file="output_obiuniq.fasta" ftype="fasta"/> 49 <output name="output" file="output_obiuniq.fasta" ftype="fasta"/>
49 </test> 50 </test>
50 <test> 51 <test expect_num_outputs="1">
51 <param name="input" value="output_ngsfilter_error_3.fastq.gz" ftype="fastqsanger.gz"/> 52 <param name="input" value="output_ngsfilter_error_3.fastq.gz" ftype="fastqsanger.gz"/>
52 <param name="options_uniq" value="family" /> 53 <param name="options_uniq" value="family"/>
53 <param name="options_attribute" value="category_attribute" /> 54 <param name="options_attribute" value="category_attribute"/>
54 <param name="mid" value="True" /> 55 <param name="mid" value="True"/>
55 <param name="prefix" value="True" /> 56 <param name="prefix" value="True"/>
56 <output name="output" file="output_obiuniq_family.fasta.gz" ftype="fasta.gz" decompress="true"/> 57 <output name="output" file="output_obiuniq_family.fasta.gz" ftype="fasta.gz" decompress="true"/>
57 </test> 58 </test>
58 </tests> 59 </tests>
60
59 <help><![CDATA[ 61 <help><![CDATA[
62
60 .. class:: infomark 63 .. class:: infomark
61 64
62 **What it does** 65 **What it does**
63 66
64 The obiuniq command is in some way analog to the standard Unix uniq -c command. 67 The obiuniq command is in some way analog to the standard Unix uniq -c command.
71 74
72 A group is defined by the sequence and optionally by the values of a set of attributes specified with the -c option. 75 A group is defined by the sequence and optionally by the values of a set of attributes specified with the -c option.
73 76
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. 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.
75 78
76 \* By default, only attributes with identical values within a group of sequence records are kept. 79 \* By default, only attributes with identical values within a group of sequence records are kept.
77 80
78 \* A count attribute is set to the total number of sequence records for each group. 81 \* A count attribute is set to the total number of sequence records for each group.
79 82
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. 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.
81 84
82 85
83 @OBITOOLS_LINK@ 86 @OBITOOLS_LINK@
84 ]]></help> 87 ]]>
88
89 </help>
85 <expand macro="citation" /> 90 <expand macro="citation" />
86 </tool> 91 </tool>