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comparison summary.qual.xml @ 0:41f5224b856b 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 05:00:52 -0400
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-1:000000000000 0:41f5224b856b
1 <tool profile="16.07" id="mothur_summary_qual" name="Summary.qual" version="@WRAPPER_VERSION@.0">
2 <description>Summarize the quality scores</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 "$qfile" qfile.dat &&
14 ln -s "$name" name.dat &&
15 ln -s "$count" count.dat &&
16
17 echo 'summary.qual(
18 qfile=qfile.dat
19 #if $name:
20 ,name=name.dat
21 #end if
22 #if $count:
23 ,count=count.dat
24 #end if
25 )'
26 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur
28 | tee mothur.out.log
29 ]]></command>
30 <inputs>
31 <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
32 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
33 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
34 </inputs>
35 <outputs>
36 <expand macro="logfile-output"/>
37 <data name="out_summary" format="mothur.summary" from_work_dir="qfile*.summary" label="${tool.name} on ${on_string}: summary"/>
38 </outputs>
39 <tests>
40 <test>
41 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/>
42 <output name="out_summary" md5="04de7c9d0f3889d5e121db9d9070c935"/>
43 <expand macro="logfile-test"/>
44 </test>
45 </tests>
46 <help>
47 <![CDATA[
48
49 @MOTHUR_OVERVIEW@
50
51 **Command Documentation**
52
53 The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information.
54
55 .. _summary.qual: https://www.mothur.org/wiki/Summary.qual
56 ]]>
57 </help>
58 <expand macro="citations"/>
59 </tool>