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comparison obiclean.xml @ 0:f4e449660000 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
author iuc
date Wed, 12 Apr 2017 17:39:09 -0400
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1 <tool id="obi_clean" name="obiclean" version="@WRAPPER_VERSION@">
2 <description>tags a set of sequences for PCR/sequencing errors identification</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8
9 <command>
10
11 <![CDATA[
12 obiclean
13
14 #if $distance
15 -d '$distance'
16 #end if
17 #if $key
18 -s '$key'
19 #end if
20 #if $ratio
21 -r '$ratio'
22 #end if
23 ${head}
24
25 '$input'>'$output'
26
27
28 ]]>
29
30 </command>
31
32 <inputs>
33 <param name="input" type="data" format="fasta" label="Input sequences file" />
34 <param name="distance" type="integer" value="1" optional="true" label="Maximum numbers of differences between two variant sequences (default: 1)" />
35 <param name="key" type="text" optional="true" label="Specify an attribute containing sample definition" />
36 <param name="ratio" optional="true" type="float" value="1" label="Threshold ratio between counts (rare/abundant counts) of two sequence records so that the less abundant one is a variant of the more abundant (default: 1, i.e. all less abundant sequences are variants)" />
37 <param name="head" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Do you want to select only sequences with the head status in a least one sample?" />
38 </inputs>
39 <outputs>
40 <data format="fasta" name="output" label="output with ${tool.name} on ${on_string}" />
41 </outputs>
42 <tests>
43 <test>
44 <param name="input" value="output_obiannotate.fasta" />
45 <param name="head" value="True"/>
46 <output name="output" file="output_obiclean_simple.fasta" ftype="fasta"/>
47 </test>
48 <test>
49 <param name="input" value="output_obiannotate.fasta" />
50 <param name="key" value="merged_sample"/>
51 <param name="ratio" value="0.05"/>
52 <param name="head" value="False"/>
53 <output name="output" file="output_obiclean_advanced.fasta" ftype="fasta"/>
54 </test>
55 </tests>
56 <help><![CDATA[
57
58 .. class:: infomark
59
60 **What it does**
61
62 obijoinpairedend aims at joining the two reads of a paired-end library.
63
64 For this purpose, it concatenates sequence merging the forward read and the reversed-complemented reverse read.
65
66 The program uses as input one or two sequences reads files.
67
68 If two files are used one of them must be specified using the -r option. Sequence records corresponding to the same read pair must be in the same order in the two files.
69 If just one file is provided, sequence records are supposed to be all of the same length. The first half of the sequence is used as forward read, the second half is used as the reverse read.
70
71 @OBITOOLS_LINK@
72
73 ]]>
74 </help>
75 <expand macro="citation" />
76 </tool>