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comparison summary.seqs.xml @ 0:a8637d3ac14a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:51:58 -0400
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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="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$fasta" fasta.dat &&
11 ln -s "$name" name.dat &&
12 ln -s "$count" count.dat &&
13
14 echo 'summary.seqs(
15 fasta=fasta.dat,
16 #if $name:
17 name=name.dat,
18 #end if
19 #if $count:
20 count=count.dat,
21 #end if
22 processors='\${GALAXY_SLOTS:-8}'
23 )'
24 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur
26 ]]></command>
27 <inputs>
28 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Dataset"/>
29 <param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/>
30 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/>
31 </inputs>
32 <outputs>
33 <expand macro="logfile-output"/>
34 <data name="out_summary" format="mothur.summary" from_work_dir="fasta*.summary" label="${tool.name} on ${on_string}: summary"/>
35 </outputs>
36 <tests>
37 <test>
38 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
39 <output name="out_summary" file="Mock_S280_L001_R1_001_small.trim.contigs.summary" ftype="mothur.summary"/>
40 <expand macro="logfile-test"/>
41 </test>
42 <test><!-- test names input -->
43 <param name="fasta" value="amazon.unique.fasta"/>
44 <param name="name" value="amazon.names"/>
45 <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
46 <expand macro="logfile-test"/>
47 </test>
48 <test><!-- test count input -->
49 <param name="fasta" value="amazon.unique.fasta"/>
50 <param name="count" value="amazon.count_table"/>
51 <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
52 <expand macro="logfile-test"/>
53 </test>
54 </tests>
55 <help>
56 <![CDATA[
57
58 @MOTHUR_OVERVIEW@
59
60 **Command Documenation**
61
62 The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
63
64
65 .. _summary.seqs: http://www.mothur.org/wiki/Summary.seqs
66 ]]>
67 </help>
68 <expand macro="citations"/>
69 </tool>