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comparison filter.shared.xml @ 0:bccb5efbc4ee 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 05:47:34 -0400
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children 644b7baba854
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-1:000000000000 0:bccb5efbc4ee
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="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
15 echo 'filter.shared(
16 shared=otu.dat,
17 #if $label:
18 label=${ str($label).replace(",","-") },
19 #end if
20 #if $label:
21 groups=${ str($groups).replace(",","-") },
22 #end if
23 minabund=$minabund,
24 minpercent=$minpercent,
25 rarepercent=$rarepercent,
26 keepties=$keepties,
27 minnumsamples=$minnumsamples,
28 minpercentsamples=$minpercentsamples,
29 mintotal=$mintotal,
30 makerare=$makerare
31 )'
32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur
34 | tee mothur.out.log
35 ]]></command>
36 <inputs>
37 <param name="otu" type="data" format="mothur.shared" label="shared - specify your shared file"/>
38 <param name="label" type="select" optional="true" multiple="true" label="label - OTU Labels" help="If none selected, all labels will be output">
39 <expand macro="labeloptions"/>
40 </param>
41 <param name="groups" type="select" optional="true" multiple="true" label="Select groups for to include in this grouping">
42 <options>
43 <filter type="data_meta" ref="otu" key="groups"/>
44 </options>
45 </param>
46 <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"/>
47 <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)"/>
48 <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)"/>
49 <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)"/>
50 <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)"/>
51 <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)"/>
52 <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)"/>
53 <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)"/>
54 </inputs>
55 <outputs>
56 <expand macro="logfile-output"/>
57 <collection name="filter_shared" type="list" label="${tool.name} on ${on_string}: filter.shared">
58 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.filter\.dat" format="mothur.shared"/>
59 </collection>
60 </outputs>
61 <tests>
62 <test><!-- test with defaults -->
63 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
64 <param name="minabund" value="1"/>
65 <output_collection name="filter_shared" count="36">
66 <element name="0.29" md5="db8387475c126110f2ac21066344c933" ftype="mothur.shared"/>
67 </output_collection>
68 <expand macro="logfile-test"/>
69 </test>
70 <test><!-- test with label and group select -->
71 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
72 <param name="label" value="0.05,0.29,0.33"/>
73 <param name="groups" value="forest,pasture"/>
74 <param name="minabund" value="1"/>
75 <output_collection name="filter_shared" count="3">
76 <element name="0.29" md5="db8387475c126110f2ac21066344c933" ftype="mothur.shared"/>
77 </output_collection>
78 <expand macro="logfile-test"/>
79 </test>
80 </tests>
81 <help>
82 <![CDATA[
83
84 @MOTHUR_OVERVIEW@
85
86 **Command Documentation**
87
88 The filter.shared_ is used to remove OTUs based on various critieria.
89
90 .. _filter.shared: https://www.mothur.org/wiki/Filter.shared
91
92 ]]>
93 </help>
94 <citations>
95 <citation type="doi">10.1128/AEM.01541-09</citation>
96 </citations>
97 </tool>