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comparison filter.shared.xml @ 0:4adf107b126e 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 16:30:40 -0400
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children 897ba33ecbdb
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1 <tool profile="16.07" id="mothur_filter_shared" name="Filter.shared" version="@WRAPPER_VERSION@.0">
2 <description>remove OTUs based on various critieria</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 "$otu" otu.dat &&
11
12 echo 'filter.shared(
13 shared=otu.dat,
14 #if $label:
15 label=${ str($label).replace(",","-") },
16 #end if
17 #if $label:
18 groups=${ str($groups).replace(",","-") },
19 #end if
20 minabund=$minabund,
21 minpercent=$minpercent,
22 rarepercent=$rarepercent,
23 keepties=$keepties,
24 minnumsamples=$minnumsamples,
25 minpercentsamples=$minpercentsamples,
26 mintotal=$mintotal,
27 makerare=$makerare
28 )'
29 | sed 's/ //g' ## mothur trips over whitespace
30 | mothur
31 ]]></command>
32 <inputs>
33 <param name="otu" type="data" format="mothur.shared" label="shared - specify your shared file"/>
34 <param name="label" type="select" optional="true" multiple="true" label="label - OTU Labels" help="If none selected, all labels will be output">
35 <expand macro="labeloptions"/>
36 </param>
37 <param name="groups" type="select" optional="true" multiple="true" label="Select groups for to include in this grouping">
38 <options>
39 <filter type="data_meta" ref="otu" key="groups"/>
40 </options>
41 </param>
42 <param name="minabund" type="integer" value="0" min="0" label="minabund - indicate the minimum abundance required for each sample in a given OTU" help="If any samples abundance falls below the minimum, the OTU is removed. Default=0"/>
43 <param name="minpercent" type="integer" value="0" min="0" max="100" label="minpercent - indicate the minimum relative abundance of an OTU" help="For example, if the OTUs total abundance across all samples is 8, and the total abundance across all OTUs is 1000, and minpercent=1. The OTU's relative abundance is 0.008, the minimum is 0.01, so the OTU will be removed (Default=0)"/>
44 <param name="rarepercent" type="integer" value="0" min="0" max="100" label="rarepercent - indicate the percentage of otus to remove" help="The OTUs chosen to be removed are the rarest. For example if you have 1000 OTUs, rarepercent=20 would remove the 200 OTUs with the lowest abundance (Default=0)"/>
45 <param name="keepties" type="boolean" truevalue="true" falsevalue="false" checked="true" label="keepties - indicate you want to keep the OTUs with the same abundance as the first 'not rare' OTU" help="For example if you have 10 OTUs, rarepercent=20 abundances of 20, 18, 15, 15, 10, 5, 3, 3, 3, 1. keepties=t, would remove the 10th OTU, but keep the 9th because its abundance ties the 8th OTU. keepties=f would remove OTUs 9 and 10 (Default=T)"/>
46 <param name="minnumsamples" type="integer" value="0" min="0" label="minnumsamples - indicate the minimum number of samples present in an OTU" help="If the number of samples present falls below the minimum, the OTU is removed (Default=0)"/>
47 <param name="minpercentsamples" type="integer" value="0" min="0" max="100" label="minpercentsamples - indicate the minimum percent of sample present in an OTU" help="For example, if the total number of samples is 10, the number present is 3, and the minpercentsamples=50. The OTU's precent of samples is 0.333, the minimum is 0.50, so the OTU will be removed (Default=0)"/>
48 <param name="mintotal" type="integer" value="0" min="0" max="100" label="mintotal - indicate the minimum abundance required for a given OTU" help="If abundance across all samples falls below the minimum, the OTU is removed (Default=0)"/>
49 <param name="makerare" type="boolean" truevalue="true" falsevalue="false" checked="true" label="makerare - indicate you want the abundances of any removed OTUs to be saved and a new rare OTU created with its abundances equal to the sum of the OTUs removed" help="This will preserve the number of reads in your dataset (Default=T)"/>
50 </inputs>
51 <outputs>
52 <expand macro="logfile-output"/>
53 <collection name="filter_shared" type="list" label="${tool.name} on ${on_string}: filter.shared">
54 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.filter\.dat" format="mothur.shared"/>
55 </collection>
56 </outputs>
57 <tests>
58 <test><!-- test with defaults -->
59 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
60 <param name="minabund" value="1"/>
61 <output_collection name="filter_shared" count="36">
62 <element name="0.29" md5="db8387475c126110f2ac21066344c933" ftype="mothur.shared"/>
63 </output_collection>
64 <expand macro="logfile-test"/>
65 </test>
66 <test><!-- test with label and group select -->
67 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
68 <param name="label" value="0.05,0.29,0.33"/>
69 <param name="groups" value="forest,pasture"/>
70 <param name="minabund" value="1"/>
71 <output_collection name="filter_shared" count="3">
72 <element name="0.29" md5="db8387475c126110f2ac21066344c933" ftype="mothur.shared"/>
73 </output_collection>
74 <expand macro="logfile-test"/>
75 </test>
76 </tests>
77 <help>
78 <![CDATA[
79
80 @MOTHUR_OVERVIEW@
81
82 **Command Documenation**
83
84 The filter.shared_ is used to remove OTUs based on various critieria.
85
86 .. _filter.shared: http://www.mothur.org/wiki/Filter.shared
87
88 ]]>
89 </help>
90 <citations>
91 <citation type="doi">10.1128/AEM.01541-09</citation>
92 </citations>
93 </tool>