Mercurial > repos > iuc > mothur_cluster_fragments

comparison cluster.fragments.xml @ 0:145595c55727 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:26:17 -0400
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1 <tool profile="16.07" id="mothur_cluster_fragments" name="Cluster.fragments" version="@WRAPPER_VERSION@.0">
2 <description> Group sequences that are part of a larger sequence</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat &&
14 ln -s "$names" names.dat &&
15 ln -s "$count" count.dat &&
16
17 echo 'cluster.fragments(
18 fasta=fasta.dat,
19 diffs=$diffs,
20 percent=$percent,
21 #if $count:
22 count=count.dat,
23 #end if
24 name=names.dat
25 )'
26 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur
28 | tee mothur.out.log
29 ]]></command>
30 <inputs>
31 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
32 <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
33 <param name="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)" min="0"/>
34 <param name="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" min="0" max="100"
35 help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge."/>
36 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
37 </inputs>
38 <outputs>
39 <expand macro="logfile-output"/>
40 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.fragclust.fasta" label="${tool.name} on ${on_string}: fasta"/>
41 <data name="out_names" format="mothur.names" from_work_dir="fasta*.fragclust.names" label="${tool.name} on ${on_string}: names"/>
42 </outputs>
43 <tests>
44 <test>
45 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
46 <param name="names" value="amazon1.names" ftype="mothur.names"/>
47 <output name="out_fasta" file="amazon.fragclust.fasta" ftype="fasta"/>
48 <output name="out_names" file="amazon.fragclust.names" ftype="mothur.names"/>
49 <expand macro="logfile-test"/>
50 </test>
51 </tests>
52 <help>
53 <![CDATA[
54
55 @MOTHUR_OVERVIEW@
56
57 **Command Documentation**
58
59 The cluster.fragments_ command groups sequences that are part of a larger sequence.
60
61 .. _cluster.fragments: https://www.mothur.org/wiki/Cluster.fragments
62
63 v1.21: Updated to Mothur 1.33. Added count parameter.
64
65 ]]>
66 </help>
67 <expand macro="citations"/>
68 </tool>