Mercurial > repos > iuc > mothur_remove_rare

comparison remove.rare.xml @ 3:39df13dda6bf 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 21:57:22 -0400
parents c90c4b4a0fae
children 189db1a23e9a
comparison
equal deleted inserted replaced
2:c90c4b4a0fae 3:39df13dda6bf
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 "$input.otu" input_otu.dat && 13 ln -s '$input.otu' input_otu.dat &&
14 #if $input.source == 'list': 14 #if $input.source == 'list':
15 ln -s "$input.group" input.group.dat && 15 ln -s '$input.group' input.group.dat &&
16 ln -s "$input.count" input.count.dat && 16 ln -s '$input.count' input.count.dat &&
17 #end if
18
19 echo 'remove.rare(
20 #if $input.otu.is_of_type("mothur.rabund"):
21 rabund=input_otu.dat,
22 #elif $input.otu.is_of_type("mothur.sabund"):
23 sabund=input_otu.dat,
24 #elif $input.otu.is_of_type("mothur.list"):
25 list=input_otu.dat,
26 #if $input.group:
27 group=input.group.dat,
17 #end if 28 #end if
18 29 #if $input.groups:
19 echo 'remove.rare( 30 groups=${ str($input.groups).replace(",","-") },
20 #if $input.otu.is_of_type("mothur.rabund"): 31 #end if
21 rabund=input_otu.dat, 32 #if $input.count:
22 #elif $input.otu.is_of_type("mothur.sabund"): 33 count=input.count.dat,
23 sabund=input_otu.dat, 34 #end if
24 #elif $input.otu.is_of_type("mothur.list"): 35 #elif $input.otu.is_of_type("mothur.shared"):
25 list=input_otu.dat, 36 shared=input_otu.dat,
26 #if $input.group: 37 bygroup=$input.bygroup,
27 group=input.group.dat, 38 #if $input.groups:
28 #end if 39 groups=${ str($input.groups).replace(",","-") },
29 #if $input.groups: 40 #end if
30 groups=${ str($input.groups).replace(",","-") }, 41 #end if
31 #end if 42 #if $input.label:
32 #if $input.count: 43 label=${ str($input.label).replace(",","-") },
33 count=input.count.dat, 44 #end if
34 #end if 45 nseqs=$nseqs
35 #elif $input.otu.is_of_type("mothur.shared"): 46 )'
36 shared=input_otu.dat, 47 | sed 's/ //g' ## mothur trips over whitespace
37 bygroup=$input.bygroup, 48 | mothur
38 #if $input.groups: 49 | tee mothur.out.log
39 groups=${ str($input.groups).replace(",","-") },
40 #end if
41 #end if
42 #if $input.label:
43 label=${ str($input.label).replace(",","-") },
44 #end if
45 nseqs=$nseqs
46 )'
47 | sed 's/ //g' ## mothur trips over whitespace
48 | mothur
49 | tee mothur.out.log
50 ]]></command> 50 ]]></command>
51 <inputs> 51 <inputs>
52 <conditional name="input"> 52 <conditional name="input">
53 <param name="source" type="select" label="Select Input Format"> 53 <param name="source" type="select" label="Select Input Format">
54 <option value="shared">shared</option> 54 <option value="shared">shared</option>
86 <expand macro="labeloptions"/> 86 <expand macro="labeloptions"/>
87 </param> 87 </param>
88 </when> 88 </when>
89 </conditional> 89 </conditional>
90 <param name="nseqs" type="integer" value="1" min="0" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/> 90 <param name="nseqs" type="integer" value="1" min="0" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/>
91 <expand macro="param-savelog"/>
91 </inputs> 92 </inputs>
92 <outputs> 93 <outputs>
93 <expand macro="logfile-output"/> 94 <expand macro="logfile-output"/>
94 <data name="pick_otu" format_source="otu" from_work_dir="input_otu*.pick.*" label="${tool.name} on ${on_string}: pick.${input.otu.ext}"> 95 <data name="pick_otu" format_source="otu" from_work_dir="input_otu*.pick.*" label="${tool.name} on ${on_string}: pick.${input.otu.ext}">
95 <filter>input['source'] != 'shared'</filter> 96 <filter>input['source'] != 'shared'</filter>
105 <tests> 106 <tests>
106 <test><!-- test with list --> 107 <test><!-- test with list -->
107 <param name="source" value="list"/> 108 <param name="source" value="list"/>
108 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 109 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
109 <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/> 110 <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/>
111 <param name="savelog" value="true"/>
110 <expand macro="logfile-test"/> 112 <expand macro="logfile-test"/>
111 </test> 113 </test>
112 <test><!-- test with list and group file --> 114 <test><!-- test with list and group file -->
113 <param name="source" value="list"/> 115 <param name="source" value="list"/>
114 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 116 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
115 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 117 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
116 <param name="groups" value="forest,pasture"/> 118 <param name="groups" value="forest,pasture"/>
117 <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/> 119 <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/>
118 <output name="pick_group" md5="9561ba470c769670ab6d92563a44027f" ftype="mothur.groups"/> 120 <output name="pick_group" md5="9561ba470c769670ab6d92563a44027f" ftype="mothur.groups"/>
121 <param name="savelog" value="true"/>
119 <expand macro="logfile-test"/> 122 <expand macro="logfile-test"/>
120 </test> 123 </test>
121 <test><!-- test with shared file --> 124 <test><!-- test with shared file -->
122 <param name="source" value="shared"/> 125 <param name="source" value="shared"/>
123 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 126 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
124 <output_collection name="pick_shared" count="36"> 127 <output_collection name="pick_shared" count="36">
125 <element name="0.38" md5="e58da633dd16f0cb6472d6c6b3318c9f" ftype="mothur.shared"/> 128 <element name="0.38" md5="e58da633dd16f0cb6472d6c6b3318c9f" ftype="mothur.shared"/>
126 </output_collection> 129 </output_collection>
130 <param name="savelog" value="true"/>
127 <expand macro="logfile-test"/> 131 <expand macro="logfile-test"/>
128 </test> 132 </test>
129 <test><!-- test with shared file and label/group select --> 133 <test><!-- test with shared file and label/group select -->
130 <param name="source" value="shared"/> 134 <param name="source" value="shared"/>
131 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 135 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
133 <param name="label" value="0.05,0.22,0.41"/> 137 <param name="label" value="0.05,0.22,0.41"/>
134 <param name="groups" value="forest,pasture"/> 138 <param name="groups" value="forest,pasture"/>
135 <output_collection name="pick_shared" count="3"> 139 <output_collection name="pick_shared" count="3">
136 <element name="0.22" md5="46d97e6f97e7909d72d09a1726655539" ftype="mothur.shared"/> 140 <element name="0.22" md5="46d97e6f97e7909d72d09a1726655539" ftype="mothur.shared"/>
137 </output_collection> 141 </output_collection>
142 <param name="savelog" value="true"/>
138 <expand macro="logfile-test"/> 143 <expand macro="logfile-test"/>
139 </test> 144 </test>
140 <test><!-- test with rabund/sabund file --> 145 <test><!-- test with rabund/sabund file -->
141 <param name="source" value="default"/> 146 <param name="source" value="default"/>
142 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/> 147 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
143 <output name="pick_otu" md5="ca842ed3ef543d3dd76fd9089cd87c46" ftype="mothur.sabund"/> 148 <output name="pick_otu" md5="ca842ed3ef543d3dd76fd9089cd87c46" ftype="mothur.sabund"/>
149 <param name="savelog" value="true"/>
144 <expand macro="logfile-test"/> 150 <expand macro="logfile-test"/>
145 </test> 151 </test>
146 </tests> 152 </tests>
147 <help> 153 <help><![CDATA[
148 <![CDATA[
149 154
150 @MOTHUR_OVERVIEW@ 155 @MOTHUR_OVERVIEW@
151 156
152 **Command Documentation** 157 **Command Documentation**
153 158
157 .. _sabund: https://www.mothur.org/wiki/Sabund_file 162 .. _sabund: https://www.mothur.org/wiki/Sabund_file
158 .. _rabund: https://www.mothur.org/wiki/Rabund_file 163 .. _rabund: https://www.mothur.org/wiki/Rabund_file
159 .. _shared: https://www.mothur.org/wiki/Shared_file 164 .. _shared: https://www.mothur.org/wiki/Shared_file
160 .. _remove.rare: https://www.mothur.org/wiki/Remove.rare 165 .. _remove.rare: https://www.mothur.org/wiki/Remove.rare
161 166
162 ]]> 167 ]]></help>
163 </help>
164 <expand macro="citations"/> 168 <expand macro="citations"/>
165 </tool> 169 </tool>