Mercurial > repos > iuc > mothur_summary_seqs

comparison summary.seqs.xml @ 0:9377122cc144 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 05:24:16 -0400
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children d68125f75fc2
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-1:000000000000 0:9377122cc144
1 <tool profile="16.07" id="mothur_summary_seqs" name="Summary.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Summarize the quality of sequences</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 "$fasta" fasta.dat &&
14 ln -s "$name" name.dat &&
15 ln -s "$count" count.dat &&
16
17 echo 'summary.seqs(
18 fasta=fasta.dat,
19 #if $name:
20 name=name.dat,
21 #end if
22 #if $count:
23 count=count.dat,
24 #end if
25 processors='\${GALAXY_SLOTS:-8}'
26 )'
27 | sed 's/ //g' ## mothur trips over whitespace
28 | mothur
29 | tee mothur.out.log
30 ]]></command>
31 <inputs>
32 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Dataset"/>
33 <param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/>
34 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/>
35 </inputs>
36 <outputs>
37 <expand macro="logfile-output"/>
38 <data name="out_summary" format="mothur.summary" from_work_dir="fasta*.summary" label="${tool.name} on ${on_string}: summary"/>
39 </outputs>
40 <tests>
41 <test>
42 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
43 <output name="out_summary" file="Mock_S280_L001_R1_001_small.trim.contigs.summary" ftype="mothur.summary"/>
44 <expand macro="logfile-test"/>
45 </test>
46 <test><!-- test names input -->
47 <param name="fasta" value="amazon.unique.fasta"/>
48 <param name="name" value="amazon.names"/>
49 <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
50 <expand macro="logfile-test"/>
51 </test>
52 <test><!-- test count input -->
53 <param name="fasta" value="amazon.unique.fasta"/>
54 <param name="count" value="amazon.count_table"/>
55 <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
56 <expand macro="logfile-test"/>
57 </test>
58 </tests>
59 <help>
60 <![CDATA[
61
62 @MOTHUR_OVERVIEW@
63
64 **Command Documentation**
65
66 The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
67
68
69 .. _summary.seqs: https://www.mothur.org/wiki/Summary.seqs
70 ]]>
71 </help>
72 <expand macro="citations"/>
73 </tool>