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comparison remove.groups.xml @ 2:75433aae83fb 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 22:03:44 -0400
parents e7a69b6134c5
children
comparison
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1:bbef0f523231 2:75433aae83fb
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 #if $groupnames.source == "other": 13 #if $groupnames.source == "other":
14 ln -s "$groupnames.group_in" groupnames_group_in.dat && 14 ln -s '$groupnames.group_in' groupnames_group_in.dat &&
15 ln -s "$groupnames.fasta_in" groupnames_fasta_in.dat && 15 ln -s '$groupnames.fasta_in' groupnames_fasta_in.dat &&
16 ln -s "$groupnames.name_in" groupnames_name_in.dat && 16 ln -s '$groupnames.name_in' groupnames_name_in.dat &&
17 ln -s "$groupnames.list_in" groupnames_list_in.dat && 17 ln -s '$groupnames.list_in' groupnames_list_in.dat &&
18 ln -s "$groupnames.taxonomy_in" groupnames_taxonomy_in.dat && 18 ln -s '$groupnames.taxonomy_in' groupnames_taxonomy_in.dat &&
19 ln -s '$groupnames.column_in' groupnames_column_in.dat &&
20 ln -s '$groupnames.phylip_in' groupnames_phylip_in.dat &&
21 #else
22 ln -s '$groupnames.shared_in' groupnames_shared_in.dat &&
23 #end if
24
25 echo 'remove.groups(
26 #if $groupnames.source == "other":
27 #if $group_in.is_of_type("mothur.groups"):
28 group=groupnames_group_in.dat
19 #else 29 #else
20 ln -s "$groupnames.shared_in" groupnames_shared_in.dat && 30 count=groupnames_group_in.dat
21 #end if 31 #end if
22 32 #if $groupnames.fasta_in:
23 echo 'remove.groups( 33 ,fasta=groupnames_fasta_in.dat
24 #if $groupnames.source == "other": 34 #end if
25 #if $group_in.is_of_type("mothur.groups"): 35 #if $groupnames.name_in:
26 group=groupnames_group_in.dat 36 ,name=groupnames_name_in.dat
27 #else 37 #end if
28 count=groupnames_group_in.dat 38 #if $groupnames.list_in:
29 #end if 39 ,list=groupnames_list_in.dat
30 #if $groupnames.fasta_in: 40 #end if
31 ,fasta=groupnames_fasta_in.dat 41 #if $groupnames.taxonomy_in:
32 #end if 42 ,taxonomy=groupnames_taxonomy_in.dat
33 #if $groupnames.name_in: 43 #end if
34 ,name=groupnames_name_in.dat 44 #if $column_in:
35 #end if 45 ,column=groupnames_column_in.dat
36 #if $groupnames.list_in: 46 #end if
37 ,list=groupnames_list_in.dat 47 #if $phylip_in:
38 #end if 48 ,phylip=groupnames_phylip_in.dat
39 #if $groupnames.taxonomy_in: 49 #end if
40 ,taxonomy=groupnames_taxonomy_in.dat 50 #else
41 #end if 51 shared=groupnames_shared_in.dat
42 #else 52 #end if
43 shared=groupnames_shared_in.dat 53 ,groups=${ str($groupnames.groups).replace(",","-") }
44 #end if 54 )'
45 ,groups=${ str($groupnames.groups).replace(",","-") } 55 | sed 's/ //g' ## mothur trips over whitespace
46 )' 56 | mothur
47 | sed 's/ //g' ## mothur trips over whitespace 57 | tee mothur.out.log
48 | mothur
49 | tee mothur.out.log
50 ]]></command> 58 ]]></command>
51 <inputs> 59 <inputs>
52 <conditional name="groupnames"> 60 <conditional name="groupnames">
53 <param name="source" type="select" label="Select Input Type"> 61 <param name="source" type="select" label="Select Input Type">
54 <option value="shared">shared file</option> 62 <option value="shared">shared file</option>
55 <option value="other">fasta, name, taxonomy, or list with a group file or count table</option> 63 <option value="other">fasta, name, taxonomy, distance matrix or list with a group file or count table</option>
56 </param> 64 </param>
57 <when value="other"> 65 <when value="other">
58 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count table - Groups"/> 66 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count table - Groups"/>
59 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false"> 67 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
60 <options> 68 <options>
63 </param> 71 </param>
64 <param name="fasta_in" type="data" format="mothur.align,fasta" optional="true" label="fasta - Fasta Sequences"/> 72 <param name="fasta_in" type="data" format="mothur.align,fasta" optional="true" label="fasta - Fasta Sequences"/>
65 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 73 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
66 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> 74 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
67 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> 75 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
76 <param name="phylip_in" type="data" format="mothur.lower.dist,mothur.square.dist" optional="true" label="phylip - Distance Matrix you would like to select distances from"
77 help="must be a phylip-formatted distance matrix"/>
78 <param name="column_in" type="data" format="mothur.pair.dist" optional="true" label="column - Distance Matrix you would like to select distances from"
79 help="must be a column-formatted distance matrix"/>
68 </when> 80 </when>
69 <when value="shared"> 81 <when value="shared">
70 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/> 82 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
71 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false"> 83 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
72 <options> 84 <options>
73 <filter type="data_meta" ref="shared_in" key="groups"/> 85 <filter type="data_meta" ref="shared_in" key="groups"/>
74 </options> 86 </options>
75 </param> 87 </param>
76 </when> 88 </when>
77 </conditional> 89 </conditional>
90 <expand macro="param-savelog"/>
78 </inputs> 91 </inputs>
79 <outputs> 92 <outputs>
80 <expand macro="logfile-output"/> 93 <expand macro="logfile-output"/>
81 <data name="fasta_out" format_source="fasta_in" from_work_dir="groupnames_fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta"> 94 <data name="fasta_out" format_source="fasta_in" from_work_dir="groupnames_fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
82 <filter>groupnames['source'] == 'other' and groupnames['fasta_in']</filter> 95 <filter>groupnames['source'] == 'other' and groupnames['fasta_in']</filter>
99 </collection> 112 </collection>
100 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: pick.shared"> 113 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: pick.shared">
101 <filter>groupnames['source'] == 'shared'</filter> 114 <filter>groupnames['source'] == 'shared'</filter>
102 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/> 115 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
103 </collection> 116 </collection>
117 <data name="phylip_out" format_source="phylip_in" from_work_dir="groupnames_phylip_in*.pick.*" label="${tool.name} on ${on_string}: pick.phylip">
118 <filter>groupnames['phylip_in']</filter>
119 </data>
120 <data name="column_out" format="mothur.pair.dist" from_work_dir="groupnames_column_in*.pick.*" label="${tool.name} on ${on_string}: pick.column">
121 <filter>groupnames['column_in']</filter>
122 </data>
104 </outputs> 123 </outputs>
105 <tests> 124 <tests>
106 <test><!-- test with shared file --> 125 <test><!-- test with shared file -->
107 <param name="source" value="shared"/> 126 <param name="source" value="shared"/>
108 <param name="shared_in" value="amazon.an.shared"/> 127 <param name="shared_in" value="amazon.an.shared"/>
109 <param name="groups" value="pasture"/> 128 <param name="groups" value="pasture"/>
110 <output_collection name="shared_out" count="36"> 129 <output_collection name="shared_out" count="36">
111 <element name="0.26" md5="c5043237225f0292ce1bfbd2766b96ea" ftype="mothur.shared"/> 130 <element name="0.26" md5="c5043237225f0292ce1bfbd2766b96ea" ftype="mothur.shared"/>
112 </output_collection> 131 </output_collection>
132 <param name="savelog" value="true"/>
113 <expand macro="logfile-test"/> 133 <expand macro="logfile-test"/>
114 </test> 134 </test>
115 <test><!-- test with group file and fasta/names/list/taxonomy files --> 135 <test><!-- test with group file and fasta/names/list/taxonomy files -->
116 <param name="source" value="other"/> 136 <param name="source" value="other"/>
117 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 137 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
123 <output name="fasta_out" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/> 143 <output name="fasta_out" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
124 <output name="taxonomy_out" md5="8fcaadcb5ad40873e270ad7e2cebe7fa" ftype="mothur.seq.taxonomy"/> 144 <output name="taxonomy_out" md5="8fcaadcb5ad40873e270ad7e2cebe7fa" ftype="mothur.seq.taxonomy"/>
125 <output name="group_out" md5="6d689ead98f3eb1af41f1a78386d0b50" ftype="mothur.groups"/> 145 <output name="group_out" md5="6d689ead98f3eb1af41f1a78386d0b50" ftype="mothur.groups"/>
126 <output name="name_out" md5="55dbcadbb414d95bae8a282a93c10e63" ftype="mothur.names"/> 146 <output name="name_out" md5="55dbcadbb414d95bae8a282a93c10e63" ftype="mothur.names"/>
127 <output_collection name="list_out" count="36"> 147 <output_collection name="list_out" count="36">
128 <element name="0.26" md5="71282909924de5f43452f1a5dbf623e8" ftype="mothur.list"/> 148 <element name="0.26" md5="3a92ef76cfdca6618b4016f14cbac5b8" ftype="mothur.list"/>
129 </output_collection> 149 </output_collection>
150 <param name="savelog" value="true"/>
151 <expand macro="logfile-test"/>
152 </test>
153 <test><!-- test with distance matrices -->
154 <param name="source" value="other"/>
155 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
156 <param name="column_in" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
157 <param name="phylip_in" value="amazon.dist" ftype="mothur.square.dist"/>
158 <param name="groups" value="pasture"/>
159 <output name="column_out" ftype="mothur.pair.dist">
160 <assert_contents>
161 <expand macro="test-column-format"/>
162 <has_text text="U68589"/>
163 </assert_contents>
164 </output>
165 <output name="phylip_out" ftype="mothur.square.dist">
166 <assert_contents>
167 <expand macro="test-dist-format"/>
168 <has_text text="U68589"/>
169 </assert_contents>
170 </output>
171 <param name="savelog" value="true"/>
130 <expand macro="logfile-test"/> 172 <expand macro="logfile-test"/>
131 </test> 173 </test>
132 </tests> 174 </tests>
133 <help><![CDATA[ 175 <help><![CDATA[
134 176
142 .. _group: https://www.mothur.org/wiki/Group_file 184 .. _group: https://www.mothur.org/wiki/Group_file
143 .. _list: https://www.mothur.org/wiki/List_file 185 .. _list: https://www.mothur.org/wiki/List_file
144 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline 186 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
145 .. _remove.groups: https://www.mothur.org/wiki/Remove.groups 187 .. _remove.groups: https://www.mothur.org/wiki/Remove.groups
146 188
147 ]]> 189 ]]></help>
148 </help>
149 <expand macro="citations"/> 190 <expand macro="citations"/>
150 </tool> 191 </tool>