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comparison summary.qual.xml @ 0:b889c8e70a45 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 16:51:35 -0400
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-1:000000000000 0:b889c8e70a45
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="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$qfile" qfile.dat &&
11 ln -s "$name" name.dat &&
12 ln -s "$count" count.dat &&
13
14 echo 'summary.qual(
15 qfile=qfile.dat
16 #if $name:
17 ,name=name.dat
18 #end if
19 #if $count:
20 ,count=count.dat
21 #end if
22 )'
23 | sed 's/ //g' ## mothur trips over whitespace
24 | mothur
25 ]]></command>
26 <inputs>
27 <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
28 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
29 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
30 </inputs>
31 <outputs>
32 <expand macro="logfile-output"/>
33 <data name="out_summary" format="mothur.summary" from_work_dir="qfile*.summary" label="${tool.name} on ${on_string}: summary"/>
34 </outputs>
35 <tests>
36 <test>
37 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/>
38 <output name="out_summary" md5="04de7c9d0f3889d5e121db9d9070c935"/>
39 <expand macro="logfile-test"/>
40 </test>
41 </tests>
42 <help>
43 <![CDATA[
44
45 @MOTHUR_OVERVIEW@
46
47 **Command Documenation**
48
49 The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information.
50
51 .. _summary.qual: http://www.mothur.org/wiki/Summary.qual
52 ]]>
53 </help>
54 <expand macro="citations"/>
55 </tool>