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comparison clustering.xml @ 3:4258854759ba draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
author iuc
date Tue, 01 Mar 2016 07:07:03 -0500
parents f29e21388219
children 576963db5f1b
comparison
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2:f29e21388219 3:4258854759ba
1 <tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.2"> 1 <tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.0">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>vsearch_macros.xml</import> 4 <import>vsearch_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 vsearch 11 vsearch
12 @GENERAL@ 12 @GENERAL@
13 13
14 #if $clustering_mode.clustering_mode_select == 'cluster_fast': 14 #if $clustering_mode.clustering_mode_select == 'cluster_fast':
15 --cluster_fast "$infile" 15 --cluster_fast "$infile"
16 #else if $clustering_mode.clustering_mode_select == 'cluster_smallmem': 16 #else if $clustering_mode.clustering_mode_select == 'cluster_smallmem':
17 --cluster_smallmem "$infile" 17 --cluster_smallmem "$infile"
18 #end if 18 #end if
19 ##--clusters STRING output each cluster to a separate FASTA file 19 ##--clusters STRING output each cluster to a separate FASTA file
20 20
21 #if $maxrejects: 21 #if $maxrejects:
22 --maxrejects "$maxrejects" 22 --maxrejects "$maxrejects"
23 #end if 23 #end if
24 #if $maxaccepts: 24 #if $maxaccepts:
57 --qmask "$qmask" 57 --qmask "$qmask"
58 #end if 58 #end if
59 $sizein 59 $sizein
60 $sizeout 60 $sizeout
61 --strand "$strand" 61 --strand "$strand"
62 $usersort 62 $usersort
63 #if $uc: 63 #if $uc:
64 --uc "$uc_outfile" 64 --uc "$uc_outfile"
65 #end if 65 #end if
66 66
67 ]]> 67 ]]>
68 </command> 68 </command>
69 <inputs> 69 <inputs>
70 <param name="infile" type="data" format="fasta" label="Select your input FASTA file" help="" /> 70 <param name="infile" type="data" format="fasta" label="Select your input FASTA file" help="" />
129 </data> 129 </data>
130 </outputs> 130 </outputs>
131 <tests> 131 <tests>
132 <test> 132 <test>
133 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" /> 133 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
134 <param name="id" value="0.99"/>
135 <param name="maxaccepts" value="1"/>
136 <param name="maxrejects" value="2"/>
137 <param name="sizeout" value=""/>
138 <param name="outputs" value="--centroids,--alnout,--blast6out,--notmatched" />
139 <output name="centroids" file="clustering_centroids_result1.fasta" ftype="fasta" />
140 <output name="blast6out" file="clustering_blast6out_result1.tab" ftype="tabular" />
141 <output name="notmatched" file="clustering_notmatched_result1.fasta" ftype="fasta" />
142 <!-- The result following result files would be too big -->
143 <!--output name="matched" file="clustering_matched_result1.fasta" ftype="fasta" /-->
144 <!--output name="alnout" file="clustering_alnout_result1.fasta" lines_diff="2" ftype="fasta" /-->
145 <!--output name="fastapairs" file="clustering_fastapairs_result1.fasta" ftype="fasta" /-->
146 <!--output name="msaout" file="clustering_msaout_result1.fasta" ftype="fasta" /-->
147 </test>
148 <test>
149 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
150 <param name="clustering_mode_select" value="cluster_smallmem"/> 134 <param name="clustering_mode_select" value="cluster_smallmem"/>
151 <param name="usersort" value="--usersort"/> 135 <param name="usersort" value="--usersort"/>
152 <param name="id" value="0.99"/> 136 <param name="id" value="0.99"/>
153 <param name="maxaccepts" value="1"/> 137 <param name="maxaccepts" value="1"/>
154 <param name="maxrejects" value="2"/> 138 <param name="maxrejects" value="2"/>
156 <param name="outputs" value="--centroids,--blast6out,--notmatched" /> 140 <param name="outputs" value="--centroids,--blast6out,--notmatched" />
157 <output name="centroids" file="clustering_centroids_result2.fasta" ftype="fasta" /> 141 <output name="centroids" file="clustering_centroids_result2.fasta" ftype="fasta" />
158 <output name="blast6out" file="clustering_blast6out_result2.tab" ftype="tabular" /> 142 <output name="blast6out" file="clustering_blast6out_result2.tab" ftype="tabular" />
159 <output name="notmatched" file="clustering_notmatched_result2.fasta" ftype="fasta" /> 143 <output name="notmatched" file="clustering_notmatched_result2.fasta" ftype="fasta" />
160 </test> 144 </test>
161 <test> 145 <test>
162 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" /> 146 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
163 <param name="clustering_mode_select" value="cluster_smallmem"/> 147 <param name="clustering_mode_select" value="cluster_smallmem"/>
164 <param name="usersort" value="--usersort"/> 148 <param name="usersort" value="--usersort"/>
165 <param name="id" value="0.99"/> 149 <param name="id" value="0.99"/>
166 <param name="maxaccepts" value="1"/> 150 <param name="maxaccepts" value="1"/>
169 <param name="outputs" value="--centroids" /> 153 <param name="outputs" value="--centroids" />
170 <param name="uc" value="--uc"/> 154 <param name="uc" value="--uc"/>
171 <output name="centroids" file="clustering_centroids_result2.fasta" ftype="fasta" /> 155 <output name="centroids" file="clustering_centroids_result2.fasta" ftype="fasta" />
172 <output name="uc_outfile" file="clustering_uc_result3.uc" ftype="tabular" /> 156 <output name="uc_outfile" file="clustering_uc_result3.uc" ftype="tabular" />
173 </test> 157 </test>
174 <test> 158 <test>
175 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" /> 159 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
176 <param name="clustering_mode_select" value="cluster_smallmem"/> 160 <param name="clustering_mode_select" value="cluster_smallmem"/>
177 <param name="usersort" value="--usersort"/> 161 <param name="usersort" value="--usersort"/>
178 <param name="id" value="0.99"/> 162 <param name="id" value="0.99"/>
179 <param name="maxaccepts" value="1"/> 163 <param name="maxaccepts" value="1"/>
181 <param name="sizeout" value="--sizeout"/> 165 <param name="sizeout" value="--sizeout"/>
182 <param name="outputs" value="--centroids" /> 166 <param name="outputs" value="--centroids" />
183 <param name="iddef" value="0"/> 167 <param name="iddef" value="0"/>
184 <output name="centroids" file="clustering_centroids_result4.fasta" ftype="fasta" /> 168 <output name="centroids" file="clustering_centroids_result4.fasta" ftype="fasta" />
185 </test> 169 </test>
186 <test> 170 <test>
187 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" /> 171 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
188 <param name="clustering_mode_select" value="cluster_fast"/> 172 <param name="clustering_mode_select" value="cluster_fast"/>
189 <param name="usersort" value="--usersort"/> 173 <param name="usersort" value="--usersort"/>
190 <param name="id" value="0.99"/> 174 <param name="id" value="0.99"/>
191 <param name="maxaccepts" value="1"/> 175 <param name="maxaccepts" value="1"/>