Mercurial > repos > iuc > mothur_get_otus

comparison get.otus.xml @ 3:73f7faafd5ee draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:19:54 -0500
parents 054caee6f6e8
children 1a1ab2e282fa
comparison
equal deleted inserted replaced
2:882d6c28b77a 3:73f7faafd5ee
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 "$otu" otu.dat && 13 ln -s '$accnos' accnos.dat &&
14 ln -s "$group_in" group_in.dat && 14 #if $list:
15 #if $groupnames.source == 'accnos': 15 ln -s '$list' list.dat &&
16 ln -s "$groupnames.accnos_in" groupnames.accnos_in.dat && 16 #end if
17 #end if 17 #if $shared:
18 ln -s '$shared' shared.dat &&
19 #end if
20 #if $constaxonomy:
21 ln -s '$constaxonomy' constaxonomy.dat &&
22 #end if
23 #if $corraxes:
24 ln -s '$corraxes' corraxes.dat &&
25 #end if
26 #if $otucorr:
27 ln -s '$otucorr' otucorr.dat &&
28 #end if
18 29
19 echo 'get.otus( 30 echo 'get.otus(
20 list=otu.dat, 31 #if $list
21 group=group_in.dat 32 list=list.dat,
22 #if $label: 33 #end if
23 ,label=${ str($label).replace(",","-") } 34 #if $shared
24 #end if 35 shared=shared.dat,
25 #if $groupnames.source == 'groups': 36 #end if
26 ,groups=${ str($groupnames.groups).replace(",","-") } 37 #if $corraxes:
27 #else 38 corraxes=corraxes.dat,
28 ,accnos=groupnames.accnos_in.dat 39 #end if
29 #end if 40 #if $otucorr:
30 )' 41 otucorr=otucorr.dat,
31 | sed 's/ //g' ## mothur trips over whitespace 42 #end if
32 | mothur 43 #if $constaxonomy
33 | tee mothur.out.log 44 constaxonomy=constaxonomy.dat,
45 #end if
46 accnos=accnos.dat
47 #if $labelsource.label:
48 ,label=${ str($labelsource.label).replace(",","-") }
49 #end if
50 )'
51 | sed 's/ //g' ## mothur trips over whitespace
52 | mothur
53 | tee mothur.out.log
34 ]]></command> 54 ]]></command>
35 <inputs> 55 <inputs>
36 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> 56 <param argument="accnos" type="data" format="mothur.accnos" label="accnos - Group Names from your history"/>
37 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Label" help="select exactly one label. If none selected, the first label in your file will be used"> 57 <param argument="list" type="data" format="mothur.list" optional="true" label="OTU List"/>
38 <expand macro="labeloptions"/> 58 <param argument="shared" type="data" format="mothur.shared" optional="true" label="OTU List OTU Shared file"/>
39 </param> 59 <param argument="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="contaxonomy - consensus taxonomy"
40 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/> 60 help="The contaxonomy file is the taxonomy file outputted by classify.otu"/>
41 <conditional name="groupnames"> 61 <param argument="otucorr" type="data" format="mothur.otu.corr" optional="true" label="OTU correlation file"
42 <param name="source" type="select" label="Select Group Names from"> 62 help="otu correlation coefficients are output by the otu.association command"/>
43 <option value="groups">A List of Group Names</option> 63 <param argument="corraxes" type="data" format="mothur.axes" optional="true" label="Correlation axes file"
44 <option value="accnos">A History Group Name Accnos Dataset</option> 64 help="correlation axes file is output by the corr.axes command"/>
65
66 <conditional name="labelsource">
67 <param name="source" type="select" label="Select a label from">
68 <option value="list"> OTU list file </option>
69 <option value="shared"> OTU shared file </option>
45 </param> 70 </param>
46 <when value="groups"> 71 <when value="list">
47 <param name="groups" type="select" multiple="true" force_select="true" label="groups - Pick groups to include"> 72 <param argument="label" type="select" optional="true" multiple="false" label="label - OTU Label"
48 <help>At least one group must be selected</help> 73 help="select exactly one label. If none selected, the first label in your file will be used">
49 <options> 74 <options>
50 <filter type="data_meta" ref="group_in" key="groups"/> 75 <filter type="data_meta" ref="list" key="labels"/>
51 </options> 76 </options>
52 </param> 77 </param>
53 </when> 78 </when>
54 <when value="accnos"> 79 <when value="shared">
55 <param name="accnos_in" type="data" format="mothur.accnos" optional="true" label="accnos - Group Names from your history"/> 80 <param argument="label" type="select" optional="true" multiple="false" label="label - OTU Label"
81 help="select exactly one label. If none selected, the first label in your file will be used">
82 <options>
83 <filter type="data_meta" ref="shared" key="labels"/>
84 </options>
85 </param>
56 </when> 86 </when>
57 </conditional> 87 </conditional>
58 </inputs> 88 </inputs>
59 <outputs> 89 <outputs>
60 <expand macro="logfile-output"/> 90 <expand macro="logfile-output"/>
61 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"/> 91 <data name="list_out" format="mothur.list" from_work_dir="list*.pick.*" label="${tool.name} on ${on_string}: pick.list">
62 <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.*" label="${tool.name} on ${on_string}: pick.list"/> 92 <filter> $list </filter>
93 </data>
94 <data name="shared_out" format="mothur.shared" from_work_dir="shared*.pick.*" label="${tool.name} on ${on_string}: pick.shared">
95 <filter> $shared </filter>
96 </data>
97 <data name="constaxonomy_out" format="mothur.cons.taxonomy" from_work_dir="constaxonomy*.pick.*" label="${tool.name} on ${on_string}: pick.cons.taxonomy">
98 <filter> $constaxonomy </filter>
99 </data>
100 <data name="otucorr_out" format="mothur.otu.corr" from_work_dir="otucorr*.pick.*" label="${tool.name} on ${on_string}: pick.otu.corr">
101 <filter> $otucorr </filter>
102 </data>
103 <data name="corraxes_out" format="mothur.axes" from_work_dir="corraxes*.pick.*" label="${tool.name} on ${on_string}: pick.axes">
104 <filter> $corraxes </filter>
105 </data>
63 </outputs> 106 </outputs>
64 <tests> 107 <tests>
65 <test><!-- test with group file --> 108 <test><!-- test with list file input and default settings -->
66 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 109 <param name="list" value="amazon.an.list" ftype="mothur.list"/>
67 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 110 <param name="accnos" value="amazon.otus.accnos" ftype="mothur.accnos"/>
68 <param name="source" value="groups"/> 111 <output name="list_out" ftype="mothur.list">
69 <param name="groups" value="forest,pasture"/> 112 <assert_contents>
70 <output name="list_out" md5="a771e0879bbb84e2764db70f66ae1277" ftype="mothur.list"/> 113 <expand macro="test-list-format"/>
71 <output name="group_out" md5="954ef97da9dcd152b912bcda19a6f96c" ftype="mothur.groups"/> 114 <has_text text="unique"/>
115 <has_text text="Otu01"/>
116 <has_text text="Otu17"/>
117 <has_text text="Otu42"/>
118 <not_has_text text="Otu43"/>
119 </assert_contents>
120 </output>
72 <expand macro="logfile-test"/> 121 <expand macro="logfile-test"/>
73 </test> 122 </test>
74 <test><!-- test with accnos file and label select --> 123 <test><!-- test with shared and otu.corr file and label select -->
75 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 124 <param name="shared" value="amazon.an.shared" ftype="mothur.shared"/>
125 <param name="accnos" value="amazon.otus.accnos" ftype="mothur.accnos"/>
76 <param name="label" value="0.03"/> 126 <param name="label" value="0.03"/>
77 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 127 <param name="source" value="shared"/>
78 <param name="source" value="accnos"/> 128 <param name="otucorr" value="amazon.an.0.03.pearson.otu.corr" ftype="mothur.cons.taxonomy"/>
79 <param name="accnos_in" value="amazon.groupaccnos" ftype="mothur.accnos"/> 129 <output name="shared_out" ftype="mothur.shared">
80 <output name="list_out" md5="2069739b1f7bbbe47cc237833450e57c" ftype="mothur.list"/> 130 <assert_contents>
81 <output name="group_out" md5="09ffabe975dc49f1bf251ea60c569526" ftype="mothur.groups"/> 131 <expand macro="test-shared-format"/>
132 <has_text text="0.03"/>
133 <has_text text="Otu01"/>
134 <has_text text="Otu17"/>
135 <has_text text="Otu42"/>
136 <not_has_text text="Otu43"/>
137 </assert_contents>
138 </output>
82 <expand macro="logfile-test"/> 139 <expand macro="logfile-test"/>
83 </test> 140 </test>
84 </tests> 141 </tests>
85 <help> 142 <help><![CDATA[
86 <![CDATA[
87 143
88 @MOTHUR_OVERVIEW@ 144 @MOTHUR_OVERVIEW@
89 145
90 **Command Documentation** 146 **Command Documentation**
91 147
92 The get.otus_ command selects otus from a list_ containing sequences from a specific group or set of groups. 148 The get.otus command selects otus from a given list.
93 149
94 .. _list: https://www.mothur.org/wiki/List_file 150 .. _list: https://www.mothur.org/wiki/List_file
95 .. _get.otus: https://www.mothur.org/wiki/Get.otus 151 .. _get.otus: https://www.mothur.org/wiki/Get.otus
96 152
97 v.1.20.0: Updated to Mothur 1.33 153 ]]></help>
98 ]]>
99 </help>
100 <expand macro="citations"/> 154 <expand macro="citations"/>
101 </tool> 155 </tool>