Mercurial > repos > iuc > mothur_remove_otus

comparison remove.otus.xml @ 2:45d51905b3b5 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 22:21:21 -0400
parents 4b07bc776ccb
children 2a833eb1005c
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1:8a1fbb8e703c 2:45d51905b3b5
1 <tool profile="16.07" id="mothur_remove_otus" name="Remove.otus" version="@WRAPPER_VERSION@.0"> 1 <tool profile="16.07" id="mothur_remove_otus" name="Remove.otus" version="@WRAPPER_VERSION@.0">
2 <description>Remove otus containing sequences from specified groups</description> 2 <description>Removes OTUs from various file formats</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
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 "$otu" otu.dat && 13 ln -s '$infile.otu' infile.otu.dat &&
14 ln -s "$group_in" group_in.dat && 14 ln -s '$accnos' accnos.dat &&
15 15
16 echo 'remove.otus( 16 echo 'remove.otus(
17 list=otu.dat, 17 #if $infile.otu.is_of_type("mothur.cons.taxonomy"):
18 label=$label, 18 constaxonomy=infile.otu.data,
19 group=group_in.dat 19 #end if
20 #if $groups: 20 #if $infile.otu.is_of_type("mothur.otu.corr"):
21 ,groups=${ str($groups).replace(",","-") } 21 otucorr=infile.otu.dat,
22 #end if 22 #end if
23 )' 23 #if $infile.otu.is_of_type("mothur.axes"):
24 | sed 's/ //g' ## mothur trips over whitespace 24 corraxes=infile.otu.dat,
25 | mothur 25 #end if
26 | tee mothur.out.log 26 #if $infile.otu.is_of_type("mothur.list"):
27 list=infile.otu.dat,
28 #end if
29 #if $infile.otu.is_of_type("mothur.shared"):
30 shared=infile.otu.dat,
31 #end if
32 #if $infile.intype == "in_shared" and $infile.label:
33 label=${ str($infile.label).replace(",","-") },
34 #end if
35 accnos=accnos.dat
36 )'
37 | sed 's/ //g' ## mothur trips over whitespace
38 | mothur
39 | tee mothur.out.log
27 ]]></command> 40 ]]></command>
28 <inputs> 41 <inputs>
29 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> 42 <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/>
30 <param name="label" type="select" label="label - OTU Labels" help="Select exactly one label"> 43 <conditional name="infile">
31 <expand macro="labeloptions"/> 44 <param name="intype" type="select" label="Which type of files will you be supplying?" help="">
32 </param> 45 <option value="in_shared">Shared or List file</option>
33 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/> 46 <option value="in_other">Constaxonomy / OtuCorr / CorrAxes file</option>
34 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" help="At least one group must be selected"> 47 </param>
35 <options> 48 <when value="in_shared">
36 <filter type="data_meta" ref="group_in" key="groups"/> 49 <param name="otu" type="data" format="mothur.list,mothur.shared" label="shared/list - allows you to input a list file you wish to select OTUs from. "/>
37 </options> 50 <param name="label" type="select" label="label - pick (one) OTU Label" optional="true" help="By default first label in your file is used">
38 </param> 51 <expand macro="labeloptions"/>
52 </param>
53 </when>
54 <when value="in_other">
55 <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/>
56 </when>
57 </conditional>
58 <expand macro="param-savelog"/>
39 </inputs> 59 </inputs>
40 <outputs> 60 <outputs>
41 <expand macro="logfile-output"/> 61 <expand macro="logfile-output"/>
42 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.dat" label="${tool.name} on ${on_string}: pick.groups"/> 62 <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${tool.name} on ${on_string}: pick"/>
43 <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.dat" label="${tool.name} on ${on_string}: pick.list"/>
44 </outputs> 63 </outputs>
45 <tests> 64 <tests>
46 <test> 65 <test><!-- test with shared/list input and label selection -->
66 <param name="accnos" value="amazon.accnos.otulabels"/>
67 <param name="intype" value="in_shared"/>
47 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 68 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
48 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 69 <param name="label" value="0.22"/>
49 <param name="groups" value="forest"/> 70 <output name="pick_out" ftype="mothur.list">
50 <param name="label" value="0.05"/> 71 <assert_contents>
51 <output name="list_out" md5="fa5b954ad8e8235dbb700af1a9d8a091" ftype="mothur.list"/> 72 <expand macro="test-list-format"/>
52 <output name="group_out" md5="3c9f6e88de0f60f2a870c8d4a9d61db8" ftype="mothur.groups"/> 73 <has_text text="U68686"/>
74 <has_text text="0.22"/>
75 <not_has_text text="0.03"/>
76 </assert_contents>
77 </output>
78 <param name="savelog" value="true"/>
79 <expand macro="logfile-test"/>
80 </test>
81 <test><!-- test with constaxonomy/otucorr/corraxes file -->
82 <param name="accnos" value="amazon.accnos.otulabels"/>
83 <param name="intype" value="in_other"/>
84 <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/>
85 <output name="pick_out" ftype="mothur.axes">
86 <assert_contents>
87 <expand macro="test-axes-format"/>
88 <has_text text="U68686"/>
89 </assert_contents>
90 </output>
91 <param name="savelog" value="true"/>
53 <expand macro="logfile-test"/> 92 <expand macro="logfile-test"/>
54 </test> 93 </test>
55 </tests> 94 </tests>
56 <help> 95 <help><![CDATA[
57 <![CDATA[
58 96
59 @MOTHUR_OVERVIEW@ 97 @MOTHUR_OVERVIEW@
60 98
61 **Command Documentation** 99 **Command Documentation**
62 100
63 The remove.otus_ command removes otus from a list_ containing sequences from a specific group or set of groups. 101 The remove.otus command removes otu labels from cons.taxonomy, corr.axes, otu.corr, shared and list files. This can be useful especially with subsampled datasets or when groups have been selected.
64 102
65 .. _list: https://www.mothur.org/wiki/List_file
66 .. _remove.otus: https://www.mothur.org/wiki/Remove.otus 103 .. _remove.otus: https://www.mothur.org/wiki/Remove.otus
67 104
68 ]]> 105 ]]></help>
69 </help>
70 <expand macro="citations"/> 106 <expand macro="citations"/>
71 </tool> 107 </tool>