Mercurial > repos > iuc > mothur_remove_rare

comparison remove.rare.xml @ 6:be26751f7d10 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 13:35:12 -0400
parents 13ef4cafa56d
children
comparison
equal deleted inserted replaced
5:0471c7a20761 6:be26751f7d10
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><![CDATA[ 153 <help><![CDATA[
148 154