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comparison get.sabund.xml @ 0:579ffc8e2b4b 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 05:36:09 -0400
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children 502c0ba699fb
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-1:000000000000 0:579ffc8e2b4b
1 <tool profile="16.07" id="mothur_get_sabund" name="Get.sabund" version="@WRAPPER_VERSION@.0">
2 <description>Get sabund from a otu list or rabund</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 "$otu" otu.dat &&
14 ln -s "$count" count.dat &&
15
16 echo 'get.sabund(
17 #if $label:
18 label=${ str($label).replace(",","-") },
19 #end if
20 #if $count:
21 count=count.dat,
22 #end if
23 #if $otu.is_of_type("mothur.list"):
24 list=otu.dat
25 #elif $otu.is_of_type("mothur.rabund"):
26 rabund=otu.dat
27 #end if
28 )'
29 | sed 's/ //g' ## mothur trips over whitespace
30 | mothur
31 | tee mothur.out.log
32 ]]></command>
33 <inputs>
34 <param name="otu" type="data" format="mothur.list,mothur.rabund" label="list,rabund - List or Rabund"/>
35 <param name="label" type="select" optional="true" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
36 <expand macro="labeloptions"/>
37 </param>
38 <param name="count" type="data" format="mothur.count_table" optional="true" help="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/>
39 </inputs>
40 <outputs>
41 <expand macro="logfile-output"/>
42 <data name="sabund" format="mothur.sabund" from_work_dir="otu*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
43 </outputs>
44 <tests>
45 <test><!-- test rabund input -->
46 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/>
47 <output name="sabund" file="amazon.an.sabund2" ftype="mothur.sabund"/>
48 <expand macro="logfile-test"/>
49 </test>
50 <test><!-- test otu list input -->
51 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
52 <param name="label" value="0.03,0.05"/>
53 <output name="sabund" file="amazon.an.sabund3" ftype="mothur.sabund"/>
54 <expand macro="logfile-test"/>
55 </test>
56 </tests>
57 <help>
58 <![CDATA[
59
60 @MOTHUR_OVERVIEW@
61
62
63 **Command Documentation**
64
65 The get.sabund_ command generates an sabund_ file from a list_ or rabund_ file.
66
67 .. _sabund: https://www.mothur.org/wiki/Sabund_file
68 .. _list: https://www.mothur.org/wiki/List_file
69 .. _rabund: https://www.mothur.org/wiki/Rabund_file
70 .. _get.sabund: https://www.mothur.org/wiki/Get.sabund
71
72 ]]>
73 </help>
74 <expand macro="citations"/>
75 </tool>