Mercurial > repos > iuc > mothur_get_rabund

comparison get.rabund.xml @ 0:fc3330ca7c70 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:09:39 -0400
parents
children d441d54fbe09
comparison
equal deleted inserted replaced
-1:000000000000 0:fc3330ca7c70
1 <tool profile="16.07" id="mothur_get_rabund" name="Get.rabund" version="@WRAPPER_VERSION@.0">
2 <description>Get rabund from a otu list or sabund</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 "$count" count.dat &&
14 ln -s "$otu" otu.dat &&
15
16 echo 'get.rabund(
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 $otu.is_of_type("mothur.sabund"):
26 sabund=otu.dat,
27 #end if
28 sorted=$sorted
29 )'
30 | sed 's/ //g' ## mothur trips over whitespace
31 | mothur
32 | tee mothur.out.log
33 ]]></command>
34 <inputs>
35 <param name="otu" type="data" format="mothur.list,mothur.sabund" label="list,sabund - List or Sabund"/>
36 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
37 <expand macro="labeloptions"/>
38 </param>
39 <param name="sorted" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sorted - sort by abundance" help="By default the data in the rabund file the same order as the OTUs in input, select to sort by abundance."/>
40 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
41 </inputs>
42 <outputs>
43 <expand macro="logfile-output"/>
44 <data name="rabund" format="mothur.rabund" from_work_dir="otu*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
45 </outputs>
46 <tests>
47 <test><!-- test sabund input -->
48 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
49 <param name="label" value="0.03,0.05"/>
50 <output name="rabund" file="amazon.an.rabund2" ftype="mothur.rabund"/>
51 <expand macro="logfile-test"/>
52 </test>
53 <test><!-- test otu list input -->
54 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
55 <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/>
56 <expand macro="logfile-test"/>
57 </test>
58 </tests>
59 <help>
60 <![CDATA[
61
62 @MOTHUR_OVERVIEW@
63
64 **Command Documentation**
65
66 The get.rabund_ command generates an rabund_ file from a list_ or sabund_ file.
67
68 .. _rabund: https://www.mothur.org/wiki/Rabund_file
69 .. _list: https://www.mothur.org/wiki/List_file
70 .. _sabund: https://www.mothur.org/wiki/Sabund_file
71 .. _get.rabund: https://www.mothur.org/wiki/Get.rabund
72
73 ]]>
74 </help>
75 <expand macro="citations"/>
76 </tool>