Mercurial > repos > iuc > mothur_pre_cluster
annotate pre.cluster.xml @ 4:baba9fff9dba draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author | iuc |
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date | Mon, 23 Apr 2018 09:38:18 -0400 |
parents | 39cfb67a03c0 |
children | fbbe2b081299 |
rev | line source |
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0
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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changeset
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1 <tool profile="16.07" id="mothur_pre_cluster" name="Pre.cluster" version="@WRAPPER_VERSION@.0"> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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2 <description>Remove sequences due to pyrosequencing errors</description> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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3 <macros> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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4 <import>macros.xml</import> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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5 </macros> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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6 <expand macro="requirements"/> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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7 <expand macro="stdio"/> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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8 <expand macro="version_command"/> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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9 <command><![CDATA[ |
2
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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10 @SHELL_OPTIONS@ |
0
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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11 |
2
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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12 ## create symlinks to input datasets |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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13 ln -s '$fasta' fasta.dat && |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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14 ln -s '$name' name.dat && |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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15 ln -s '$group' group.dat && |
0
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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16 |
2
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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17 echo 'pre.cluster( |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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18 fasta=fasta.dat, |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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19 #if $name.is_of_type("mothur.names"): |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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20 name=name.dat, |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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21 #elif $name.is_of_type("mothur.count_table"): |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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22 count=name.dat, |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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23 #end if |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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24 #if $group: |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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25 group=group.dat, |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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26 #end if |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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27 diffs=$diffs, |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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28 match=$match, |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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29 mismatch=$mismatch, |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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30 gapopen=$gapopen, |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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31 gapextend=$gapextend, |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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32 topdown=$topdown, |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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33 processors='\${GALAXY_SLOTS:-8}' |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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34 )' |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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35 | sed 's/ //g' ## mothur trips over whitespace |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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36 | mothur |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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37 | tee mothur.out.log && |
0
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
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38 |
2
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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39 cat fasta* && |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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40 |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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41 if [ -f fasta.precluster.map ]; then mv fasta.precluster.map fasta.precluster.fasta.map; fi |
0
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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42 ]]></command> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff
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43 <inputs> |
2
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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44 <param argument="fasta" type="data" format="fasta" label="fasta - Sequence Fasta"/> |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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45 <param argument="name" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Name reference"/> |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
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46 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
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47 <param argument="diffs" type="integer" value="1" min="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 1)"/> |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
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48 <param argument="match" type="integer" value="1" label="match - reward for a match (default 1)"/> |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
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49 <param argument="mismatch" type="integer" value="-1" label="mismatch - penalty for a mismatch (default -1)"/> |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
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50 <param argument="gapopen" type="integer" value="-2" label="gapopen - penalty for opening a gap (default -2)"/> |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
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51 <param argument="gapextend" type="integer" value="-1" label="gapextend - penalty for extending a gap (default -1)"/> |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
diff
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52 <param argument="topdown" type="boolean" truevalue="true" falsevalue="false" checked="true" label="topdown" |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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53 help="cluster from largest abundance to smallest or vice versa. Default=Yes, meaning largest to smallest"/> |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
0
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54 <expand macro="param-savelog"/> |
0
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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55 </inputs> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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56 <outputs> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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57 <expand macro="logfile-output"/> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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58 <data name="fasta_out" format_source="fasta" from_work_dir="fasta*.precluster.dat" label="${tool.name} on ${on_string}: precluster.fasta"/> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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59 <data name="names_out" format="mothur.names" from_work_dir="fasta*.precluster.names" label="${tool.name} on ${on_string}: precluster.names"> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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60 <filter>name.ext != "mothur.count_table"</filter> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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61 </data> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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62 <data name="count_out" format="mothur.count_table" from_work_dir="fasta*.precluster.count_table" label="${tool.name} on ${on_string}: precluster.count_table"> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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63 <filter>name.ext == "mothur.count_table"</filter> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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64 </data> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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65 <collection name="map_out" type="list" label="${tool.name} on ${on_string}: precluster.map"> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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66 <discover_datasets pattern="fasta\.precluster\.(?P<designation>.*)\.map" format="tabular"/> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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67 </collection> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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68 </outputs> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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69 <tests> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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70 <test><!-- test with fasta and names file --> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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71 <param name="fasta" value="amazon.fasta_head" ftype="fasta"/> |
cad74a5a9a6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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72 <param name="name" value="amazon.head.names" ftype="mothur.names"/> |
2
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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73 <output name="fasta_out" ftype="fasta"> |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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74 <assert_contents> |
39cfb67a03c0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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75 <expand macro="test-fasta-format"/> |
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76 <has_text text="U68589"/> |
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77 </assert_contents> |
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78 </output> |
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79 <output name="names_out" ftype="mothur.names"> |
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80 <assert_contents> |
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81 <expand macro="test-names-format"/> |
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82 <has_line_matching expression="^U68589\tU68589$"/> |
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83 </assert_contents> |
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84 </output> |
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85 <output_collection name="map_out" count="1"> |
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86 <element name="fasta" ftype="tabular"> |
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87 <assert_contents> |
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88 <has_text text="ideal_seq_1"/> |
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89 <has_text text="U68589"/> |
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90 </assert_contents> |
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91 </element> |
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92 </output_collection> |
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93 <param name="savelog" value="true"/> |
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94 <expand macro="logfile-test"/> |
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95 </test> |
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96 <test><!-- test with fasta and count table --> |
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97 <param name="fasta" value="amazon.fasta_head" ftype="fasta"/> |
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98 <param name="name" value="amazon.count_table" ftype="mothur.count_table"/> |
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99 <output name="fasta_out" ftype="fasta"> |
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100 <assert_contents> |
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101 <expand macro="test-fasta-format"/> |
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102 <has_text text="U68589"/> |
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103 </assert_contents> |
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104 </output> |
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105 <output name="count_out" ftype="mothur.count_table"> |
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106 <assert_contents> |
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107 <expand macro="test-count-format"/> |
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108 <has_text text="U68589"/> |
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109 </assert_contents> |
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110 </output> |
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111 <output_collection name="map_out" count="1"> |
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112 <element name="fasta" ftype="tabular"> |
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113 <assert_contents> |
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114 <has_text text="ideal_seq_1"/> |
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115 <has_text text="U68589"/> |
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116 </assert_contents> |
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117 </element> |
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118 </output_collection> |
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119 <param name="savelog" value="true"/> |
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120 <expand macro="logfile-test"/> |
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121 </test> |
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122 </tests> |
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123 <help><![CDATA[ |
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124 |
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125 @MOTHUR_OVERVIEW@ |
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126 |
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127 **Command Documentation** |
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128 |
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129 The pre.cluster_ command implements a pseudo-single linkage algorithm with the goal of removing sequences that |
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130 are likely due to pyrosequencing errors. The basic idea is that abundant sequences are more likely to generate |
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131 erroneous sequences than rare sequences. With that in mind, the algorithm proceeds by ranking sequences in order |
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132 of their abundance. Then we walk through the list of sequences looking for rarer sequences that are within some |
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133 threshold of the original sequence. Those that are within the threshold are merged with the larger sequence. |
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134 The original Huse method performs this task on a distance matrix, whereas we do it based on the original sequences. |
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135 The advantage of our approach is that the algorithm works on aligned sequences instead of a distance matrix. |
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136 This is advantageous because by pre-clustering you remove a large number of sequences making the distance |
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137 calculation much faster. |
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138 |
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139 .. _pre.cluster: https://www.mothur.org/wiki/Pre.cluster |
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140 |
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141 v1.24.0: Updated to mothur 1.33, added count and topdown parameter |
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142 |
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143 ]]></help> |
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144 <expand macro="citations"/> |
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145 </tool> |