Mercurial > repos > iuc > mothur_cluster_fragments

annotate cluster.fragments.xml @ 5:881f9a4013a9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
author iuc
date Fri, 03 Aug 2018 14:45:18 -0400
parents 19bb0a1a459e
children 7b96c990a457
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1 <tool profile="16.07" id="mothur_cluster_fragments" name="Cluster.fragments" version="@WRAPPER_VERSION@.0">
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2 <description> Group sequences that are part of a larger sequence</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$fasta' fasta.dat &&
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$names' names.dat &&
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$count' count.dat &&
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16
2
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17 echo 'cluster.fragments(
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 fasta=fasta.dat,
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 diffs=$diffs,
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 percent=$percent,
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 #if $count:
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22 count=count.dat,
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 #end if
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 name=names.dat
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25 )'
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26 | sed 's/ //g' ## mothur trips over whitespace
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 | mothur
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28 | tee mothur.out.log
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29 ]]></command>
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30 <inputs>
2
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31 <param argument="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 <param argument="names" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 <param argument="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)" min="0"/>
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 <param argument="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" min="0" max="100"
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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36 than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like:
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge."/>
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38 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
19bb0a1a459e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 <expand macro="param-savelog"/>
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40 </inputs>
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41 <outputs>
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42 <expand macro="logfile-output"/>
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43 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.fragclust.fasta" label="${tool.name} on ${on_string}: fasta"/>
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44 <data name="out_names" format="mothur.names" from_work_dir="fasta*.fragclust.names" label="${tool.name} on ${on_string}: names"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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49 <param name="names" value="amazon1.names" ftype="mothur.names"/>
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50 <output name="out_fasta" file="amazon.fragclust.fasta" ftype="fasta"/>
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51 <output name="out_names" file="amazon.fragclust.names" ftype="mothur.names"/>
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52 <param name="savelog" value="true"/>
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53 <expand macro="logfile-test"/>
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54 </test>
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55 </tests>
2
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56 <help><![CDATA[
0
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57
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58 @MOTHUR_OVERVIEW@
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59
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60 **Command Documentation**
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61
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62 The cluster.fragments_ command groups sequences that are part of a larger sequence.
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63
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64 .. _cluster.fragments: https://www.mothur.org/wiki/Cluster.fragments
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65
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66 v1.21: Updated to Mothur 1.33. Added count parameter.
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67
2
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68 ]]></help>
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69 <expand macro="citations"/>
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70 </tool>