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comparison filter.shared.xml @ 2:644b7baba854 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 22:11:33 -0400
parents bccb5efbc4ee
children e44c38a17c7a
comparison
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1:6cca4d09073c 2:644b7baba854
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 "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 14
15 echo 'filter.shared( 15 echo 'filter.shared(
16 shared=otu.dat, 16 shared=otu.dat,
17 #if $label: 17 #if $label:
18 label=${ str($label).replace(",","-") }, 18 label=${ str($label).replace(",","-") },
19 #end if 19 #end if
20 #if $label: 20 #if $label:
21 groups=${ str($groups).replace(",","-") }, 21 groups=${ str($groups).replace(",","-") },
22 #end if 22 #end if
23 minabund=$minabund, 23 minabund=$minabund,
24 minpercent=$minpercent, 24 minpercent=$minpercent,
25 rarepercent=$rarepercent, 25 rarepercent=$rarepercent,
26 keepties=$keepties, 26 keepties=$keepties,
27 minnumsamples=$minnumsamples, 27 minnumsamples=$minnumsamples,
28 minpercentsamples=$minpercentsamples, 28 minpercentsamples=$minpercentsamples,
29 mintotal=$mintotal, 29 mintotal=$mintotal,
30 makerare=$makerare 30 makerare=$makerare
31 )' 31 )'
32 | sed 's/ //g' ## mothur trips over whitespace 32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur 33 | mothur
34 | tee mothur.out.log 34 | tee mothur.out.log
35 ]]></command> 35 ]]></command>
36 <inputs> 36 <inputs>
37 <param name="otu" type="data" format="mothur.shared" label="shared - specify your shared file"/> 37 <param name="otu" argument="shared" 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"> 38 <param argument="label" type="select" optional="true" multiple="true" label="label - OTU Labels" help="If none selected, all labels will be output">
39 <expand macro="labeloptions"/> 39 <expand macro="labeloptions"/>
40 </param> 40 </param>
41 <param name="groups" type="select" optional="true" multiple="true" label="Select groups for to include in this grouping"> 41 <param argument="groups" type="select" optional="true" multiple="true" label="Select groups for to include in this grouping">
42 <options> 42 <options>
43 <filter type="data_meta" ref="otu" key="groups"/> 43 <filter type="data_meta" ref="otu" key="groups"/>
44 </options> 44 </options>
45 </param> 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"/> 46 <param argument="minabund" type="integer" value="0" min="0" label="minabund - indicate the minimum abundance required for each sample in a given OTU"
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)"/> 47 help="If any samples abundance falls below the minimum, the OTU is removed"/>
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)"/> 48 <param argument="minpercent" type="integer" value="0" min="0" max="100" label="minpercent - indicate the minimum relative abundance of an OTU"
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)"/> 49 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.
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)"/> 50 The OTU's relative abundance is 0.008, the minimum is 0.01, so the OTU will be removed"/>
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)"/> 51 <param argument="rarepercent" type="integer" value="0" min="0" max="100" label="rarepercent - indicate the percentage of otus to remove"
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)"/> 52 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"/>
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)"/> 53 <param argument="keepties" type="boolean" truevalue="true" falsevalue="false" checked="true"
54 label="keepties - indicate you want to keep the OTUs with the same abundance as the first 'not rare' OTU"
55 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,
56 but keep the 9th because its abundance ties the 8th OTU. keepties=f would remove OTUs 9 and 10"/>
57 <param argument="minnumsamples" type="integer" value="0" min="0" label="minnumsamples - indicate the minimum number of samples present in an OTU"
58 help="If the number of samples present falls below the minimum, the OTU is removed"/>
59 <param argument="minpercentsamples" type="integer" value="0" min="0" max="100" label="minpercentsamples - indicate the minimum percent of sample present in an OTU"
60 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,
61 the minimum is 0.50, so the OTU will be removed (Default=0)"/>
62 <param argument="mintotal" type="integer" value="0" min="0" max="100" label="mintotal - indicate the minimum abundance required for a given OTU"
63 help="If abundance across all samples falls below the minimum, the OTU is removed"/>
64 <param argument="makerare" type="boolean" truevalue="true" falsevalue="false" checked="true"
65 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"
66 help="This will preserve the number of reads in your dataset"/>
67 <expand macro="param-savelog"/>
54 </inputs> 68 </inputs>
55 <outputs> 69 <outputs>
56 <expand macro="logfile-output"/> 70 <expand macro="logfile-output"/>
57 <collection name="filter_shared" type="list" label="${tool.name} on ${on_string}: filter.shared"> 71 <collection name="filter_shared" type="list" label="${tool.name} on ${on_string}: filter.shared">
58 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.filter\.dat" format="mothur.shared"/> 72 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.filter\.dat" format="mothur.shared"/>
59 </collection> 73 </collection>
60 </outputs> 74 </outputs>
61 <tests> 75 <tests>
62 <test><!-- test with defaults --> 76 <test><!-- test with defaults -->
63 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 77 <param name="otu" value="esophagus.fn.shared" ftype="mothur.shared"/>
64 <param name="minabund" value="1"/> 78 <output_collection name="filter_shared" count="4">
65 <output_collection name="filter_shared" count="36"> 79 <element name="0.03" ftype="mothur.shared">
66 <element name="0.29" md5="db8387475c126110f2ac21066344c933" ftype="mothur.shared"/> 80 <assert_contents>
81 <expand macro="test-shared-format"/>
82 <has_text text="0.03"/>
83 </assert_contents>
84 </element>
67 </output_collection> 85 </output_collection>
86 <param name="savelog" value="true"/>
68 <expand macro="logfile-test"/> 87 <expand macro="logfile-test"/>
69 </test> 88 </test>
70 <test><!-- test with label and group select --> 89 <test><!-- test with label and group select -->
71 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 90 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
72 <param name="label" value="0.05,0.29,0.33"/> 91 <param name="label" value="0.05,0.29,0.33"/>
73 <param name="groups" value="forest,pasture"/> 92 <param name="groups" value="forest,pasture"/>
74 <param name="minabund" value="1"/> 93 <param name="minabund" value="1"/>
75 <output_collection name="filter_shared" count="3"> 94 <output_collection name="filter_shared" count="3">
76 <element name="0.29" md5="db8387475c126110f2ac21066344c933" ftype="mothur.shared"/> 95 <element name="0.29" ftype="mothur.shared">
96 <assert_contents>
97 <expand macro="test-shared-format"/>
98 <has_text text="0.29"/>
99 </assert_contents>
100 </element>
77 </output_collection> 101 </output_collection>
102 <param name="savelog" value="true"/>
78 <expand macro="logfile-test"/> 103 <expand macro="logfile-test"/>
79 </test> 104 </test>
80 </tests> 105 </tests>
81 <help> 106 <help><![CDATA[
82 <![CDATA[
83 107
84 @MOTHUR_OVERVIEW@ 108 @MOTHUR_OVERVIEW@
85 109
86 **Command Documentation** 110 **Command Documentation**
87 111
88 The filter.shared_ is used to remove OTUs based on various critieria. 112 The filter.shared_ is used to remove OTUs based on various critieria.
89 113
90 .. _filter.shared: https://www.mothur.org/wiki/Filter.shared 114 .. _filter.shared: https://www.mothur.org/wiki/Filter.shared
91 115
92 ]]> 116 ]]></help>
93 </help>
94 <citations> 117 <citations>
95 <citation type="doi">10.1128/AEM.01541-09</citation> 118 <citation type="doi">10.1128/AEM.01541-09</citation>
96 </citations> 119 </citations>
97 </tool> 120 </tool>