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comparison summary.qual.xml @ 2:a40036faabe8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:12:40 -0400
parents 41f5224b856b
children
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1:7c41969ad778 2:a40036faabe8
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$qfile" qfile.dat && 13 ln -s '$qfile' qfile.dat &&
14 ln -s "$name" name.dat && 14 ln -s '$name' name.dat &&
15 ln -s "$count" count.dat && 15 ln -s '$count' count.dat &&
16 16
17 echo 'summary.qual( 17 echo 'summary.qual(
18 qfile=qfile.dat 18 qfile=qfile.dat
19 #if $name: 19 #if $name:
20 ,name=name.dat 20 ,name=name.dat
21 #end if 21 #end if
22 #if $count: 22 #if $count:
23 ,count=count.dat 23 ,count=count.dat
24 #end if 24 #end if
25 )' 25 )'
26 | sed 's/ //g' ## mothur trips over whitespace 26 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur 27 | mothur
28 | tee mothur.out.log 28 | tee mothur.out.log
29 ]]></command> 29 ]]></command>
30 <inputs> 30 <inputs>
31 <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/> 31 <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
32 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/> 32 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
33 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 33 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
34 <expand macro="param-savelog"/>
34 </inputs> 35 </inputs>
35 <outputs> 36 <outputs>
36 <expand macro="logfile-output"/> 37 <expand macro="logfile-output"/>
37 <data name="out_summary" format="mothur.summary" from_work_dir="qfile*.summary" label="${tool.name} on ${on_string}: summary"/> 38 <data name="out_summary" format="mothur.summary" from_work_dir="qfile*.summary" label="${tool.name} on ${on_string}: summary"/>
38 </outputs> 39 </outputs>
39 <tests> 40 <tests>
40 <test> 41 <test>
41 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/> 42 <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/>
42 <output name="out_summary" md5="04de7c9d0f3889d5e121db9d9070c935"/> 43 <output name="out_summary" md5="04de7c9d0f3889d5e121db9d9070c935"/>
44 <param name="savelog" value="true"/>
43 <expand macro="logfile-test"/> 45 <expand macro="logfile-test"/>
44 </test> 46 </test>
45 </tests> 47 </tests>
46 <help> 48 <help><![CDATA[
47 <![CDATA[
48 49
49 @MOTHUR_OVERVIEW@ 50 @MOTHUR_OVERVIEW@
50 51
51 **Command Documentation** 52 **Command Documentation**
52 53
53 The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information. 54 The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information.
54 55
55 .. _summary.qual: https://www.mothur.org/wiki/Summary.qual 56 .. _summary.qual: https://www.mothur.org/wiki/Summary.qual
56 ]]> 57
57 </help> 58 ]]></help>
58 <expand macro="citations"/> 59 <expand macro="citations"/>
59 </tool> 60 </tool>