Mercurial > repos > iuc > vsearch
comparison clustering.xml @ 3:4258854759ba draft
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 |
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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"/> |