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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 13:15:59 +0000
parents e614dcabd870
children
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3:e614dcabd870 4:b6d9ea2fb41b
1 <tool id="obi_sort" name="obisort" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="obi_sort" name="obisort" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>sorts sequence records according to the value of a given attribute</description> 2 <description>sorts sequence records according to the value of a given attribute</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <expand macro="stdio"/> 8 <expand macro="stdio"/>
8 9
9 <command><![CDATA[ 10 <command><![CDATA[
10 @GUNZIP_INPUT@ 11 @GUNZIP_INPUT@
11 obisort 12 obisort
12 --without-progress-bar 13 --without-progress-bar
14 #if $key:
13 -k '$key' 15 -k '$key'
16 #end if
14 ${reverse} 17 ${reverse}
15 @INPUT_FORMAT@ 18 @INPUT_FORMAT@
16 @OUT_FORMAT@ 19 @OUT_FORMAT@
17 input 20 input
18 @GZIP_OUTPUT@ 21 @GZIP_OUTPUT@
19 > '$output' 22 > '$output'
20 @GENERATE_GALAXY_JSON@ 23 @GENERATE_GALAXY_JSON@
21 ]]></command> 24 ]]></command>
22 <inputs> 25 <inputs>
23 <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" /> 26 <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file"/>
24 <param name="key" type="text" label="key"/> 27 <param
25 <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" /> 28 name="key"
29 type="text"
30 label="Key"
31 help="This key must be encoded in your FASTA/FASTQ headers as key=value. See help (below) for more information."
32 optional="false"/>
33 <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Sort in reverse order?" />
26 <expand macro="input_format_options_macro"/> 34 <expand macro="input_format_options_macro"/>
27 <expand macro="out_format_macro"/> 35 <expand macro="out_format_macro"/>
28 </inputs> 36 </inputs>
29 <outputs> 37 <outputs>
30 <data format="auto" name="output"/> 38 <data format="auto" name="output"/>
31 </outputs> 39 </outputs>
32 <tests> 40 <tests>
33 <test> 41 <test expect_num_outputs="1">
34 <param name="input" value="output_obiclean_advanced.fasta" /> 42 <param name="input" value="output_obiclean_advanced.fasta" />
35 <param name="key" value="count"/> 43 <param name="key" value="count"/>
36 <param name="reverse" value="False"/> 44 <param name="reverse" value="False"/>
37 <param name="out_format" value="fasta"/> 45 <param name="out_format" value="fasta"/>
38 <output name="output" file="output_obisort.fasta" ftype="fasta"/> 46 <output name="output" file="output_obisort.fasta" ftype="fasta"/>
39 </test> 47 </test>
40 <test> 48 <test expect_num_outputs="1">
41 <param name="input" value="output_obiclean_advanced.fasta" /> 49 <param name="input" value="output_obiclean_advanced.fasta" />
42 <param name="key" value="count"/> 50 <param name="key" value="count"/>
43 <param name="reverse" value="True"/> 51 <param name="reverse" value="True"/>
44 <param name="out_format" value="fastq"/> 52 <param name="out_format" value="fastq"/>
45 <output name="output" file="output_obisort.fastq" ftype="fastqsanger"/> 53 <output name="output" file="output_obisort.fastq" ftype="fastqsanger"/>
53 61
54 obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric. 62 obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric.
55 63
56 @OBITOOLS_LINK@ 64 @OBITOOLS_LINK@
57 65
58 ]]> 66 **Inputs:**
59 67
68 For sorting by key, the input file must be in the
69 `OBITools FASTA/FASTQ format <https://pythonhosted.org/OBITools/attributes.html>`_.
70 If your file is an OBITools output, it should already be formatted correctly.
71
72 For FASTA files, your headers should look like this::
73
74 >my_sequence taxid=3456; direct=True; sample=A354; this is my pretty sequence
75 ACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT
76 GTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT
77 AACGACGTTGCAGTACGTTGCAGT
78
79 Where ``taxid``, ``direct``, and ``sample`` are keys that can be used for sorting.
80
81 If your sequences don't have title, you can format the headers with a trailing semicolon like so::
82
83 >my_sequence key1=value1;
84
85 For sorting OBITools output files, a list of OBITools sequence attributes are documented
86 `here <https://pythonhosted.org/OBITools/attributes.html#names-reserved-for-attributes>`_.
87
88 ]]>
60 </help> 89 </help>
61 <expand macro="citation" /> 90 <expand macro="citation" />
62 </tool> 91 </tool>