Mercurial > repos > iuc > mothur_get_rabund

comparison get.rabund.xml @ 2:d441d54fbe09 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 22:24:06 -0400
parents fc3330ca7c70
children
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1:abe4ffadab83 2:d441d54fbe09
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 "$count" count.dat && 13 ln -s '$count' count.dat &&
14 ln -s "$otu" otu.dat && 14 ln -s '$otu' otu.dat &&
15 15
16 echo 'get.rabund( 16 echo 'get.rabund(
17 #if $label: 17 #if $label:
18 label=${ str($label).replace(",","-") }, 18 label=${ str($label).replace(",","-") },
19 #end if 19 #end if
20 #if $count: 20 #if $count:
21 count=count.dat, 21 count=count.dat,
22 #end if 22 #end if
23 #if $otu.is_of_type("mothur.list"): 23 #if $otu.is_of_type("mothur.list"):
24 list=otu.dat, 24 list=otu.dat,
25 #elif $otu.is_of_type("mothur.sabund"): 25 #elif $otu.is_of_type("mothur.sabund"):
26 sabund=otu.dat, 26 sabund=otu.dat,
27 #end if 27 #end if
28 sorted=$sorted 28 sorted=$sorted
29 )' 29 )'
30 | sed 's/ //g' ## mothur trips over whitespace 30 | sed 's/ //g' ## mothur trips over whitespace
31 | mothur 31 | mothur
32 | tee mothur.out.log 32 | tee mothur.out.log
33 ]]></command> 33 ]]></command>
34 <inputs> 34 <inputs>
35 <param name="otu" type="data" format="mothur.list,mothur.sabund" label="list,sabund - List or Sabund"/> 35 <param name="otu" type="data" format="mothur.list,mothur.sabund" label="list,sabund - List or Sabund"/>
36 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> 36 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
37 <expand macro="labeloptions"/> 37 <expand macro="labeloptions"/>
38 </param> 38 </param>
39 <param name="sorted" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sorted - sort by abundance" help="By default the data in the rabund file the same order as the OTUs in input, select to sort by abundance."/> 39 <param name="sorted" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sorted - sort by abundance"
40 help="By default the data in the rabund file the same order as the OTUs in input, select to sort by abundance."/>
40 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 41 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
42 <expand macro="param-savelog"/>
41 </inputs> 43 </inputs>
42 <outputs> 44 <outputs>
43 <expand macro="logfile-output"/> 45 <expand macro="logfile-output"/>
44 <data name="rabund" format="mothur.rabund" from_work_dir="otu*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> 46 <data name="rabund" format="mothur.rabund" from_work_dir="otu*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
45 </outputs> 47 </outputs>
46 <tests> 48 <tests>
47 <test><!-- test sabund input --> 49 <test><!-- test sabund input -->
48 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/> 50 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
49 <param name="label" value="0.03,0.05"/> 51 <param name="label" value="0.03,0.05"/>
50 <output name="rabund" file="amazon.an.rabund2" ftype="mothur.rabund"/> 52 <output name="rabund" file="amazon.an.rabund2" ftype="mothur.rabund"/>
53 <param name="savelog" value="true"/>
51 <expand macro="logfile-test"/> 54 <expand macro="logfile-test"/>
52 </test> 55 </test>
53 <test><!-- test otu list input --> 56 <test><!-- test otu list input -->
54 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 57 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
55 <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/> 58 <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/>
59 <param name="savelog" value="true"/>
56 <expand macro="logfile-test"/> 60 <expand macro="logfile-test"/>
57 </test> 61 </test>
58 </tests> 62 </tests>
59 <help> 63 <help><![CDATA[
60 <![CDATA[
61 64
62 @MOTHUR_OVERVIEW@ 65 @MOTHUR_OVERVIEW@
63 66
64 **Command Documentation** 67 **Command Documentation**
65 68
68 .. _rabund: https://www.mothur.org/wiki/Rabund_file 71 .. _rabund: https://www.mothur.org/wiki/Rabund_file
69 .. _list: https://www.mothur.org/wiki/List_file 72 .. _list: https://www.mothur.org/wiki/List_file
70 .. _sabund: https://www.mothur.org/wiki/Sabund_file 73 .. _sabund: https://www.mothur.org/wiki/Sabund_file
71 .. _get.rabund: https://www.mothur.org/wiki/Get.rabund 74 .. _get.rabund: https://www.mothur.org/wiki/Get.rabund
72 75
73 ]]> 76 ]]></help>
74 </help>
75 <expand macro="citations"/> 77 <expand macro="citations"/>
76 </tool> 78 </tool>