Mercurial > repos > iuc > mothur_pre_cluster

annotate pre.cluster.xml @ 0:4b5b8a603f52 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:45:27 -0400
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children e277ab688993
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4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_pre_cluster" name="Pre.cluster" version="@WRAPPER_VERSION@.0">
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2 <description>Remove sequences due to pyrosequencing errors</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="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$fasta" fasta.dat &&
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$name" name.dat &&
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$group" group.dat &&
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13
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14 echo 'pre.cluster(
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 fasta=fasta.dat,
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #if $name.is_of_type("mothur.names"):
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 name=name.dat,
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 #elif $name.is_of_type("mothur.count_table"):
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 count=name.dat,
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 #end if
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21 #if $group:
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 group=group.dat,
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 #end if
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 diffs=$diffs,
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 topdown=$topdown,
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 processors='\${GALAXY_SLOTS:-8}'
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 )'
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28 | sed 's/ //g' ## mothur trips over whitespace
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 | mothur
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30 ]]></command>
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31 <inputs>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <param name="fasta" type="data" format="fasta" label="fasta - Sequence Fasta"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 <param name="name" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table- Sequences Name reference"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <param name="diffs" type="integer" value="1" min="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 1)"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <param name="topdown" type="boolean" truevalue="true" falsevalue="false" checked="false" label="allows you to specify whether to cluster from largest abundance to smallest or vice versa. Default =T, which is largest to smallest"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 </inputs>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <outputs>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <expand macro="logfile-output"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <data name="fasta_out" format_source="fasta" from_work_dir="fasta*.precluster.dat" label="${tool.name} on ${on_string}: precluster.fasta"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <data name="names_out" format="mothur.names" from_work_dir="fasta*.precluster.names" label="${tool.name} on ${on_string}: precluster.names"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <data name="map_out" format="tabular" from_work_dir="fasta*.precluster.map" label="${tool.name} on ${on_string}: precluster.map"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 </outputs>
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44 <tests>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <test><!-- test with fasta and names file -->
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 <param name="fasta" value="amazon.fasta_head" ftype="fasta"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 <param name="name" value="amazon.head.names" ftype="mothur.names"/>
4b5b8a603f52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 <output name="fasta_out" md5="d5d37ace0f2a5c020edd0aa9eb7aca9b" ftype="fasta"/>
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49 <output name="names_out" md5="51090fe5e111920ec1003c2073532d96" ftype="mothur.names"/>
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50 <output name="map_out" md5="c2ca7b0d45aa3881c7bd5cb8a44c853b" ftype="tabular"/>
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51 <expand macro="logfile-test"/>
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52 </test>
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53 </tests>
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54 <help>
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55 <![CDATA[
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56
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57 @MOTHUR_OVERVIEW@
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58
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59 **Command Documenation**
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60
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61 The pre.cluster_ command implements a pseudo-single linkage algorithm with the goal of removing sequences that are likely due to pyrosequencing errors. The basic idea is that abundant sequences are more likely to generate erroneous sequences than rare sequences. With that in mind, the algorithm proceeds by ranking sequences in order of their abundance. Then we walk through the list of sequences looking for rarer sequences that are within some threshold of the original sequence. Those that are within the threshold are merged with the larger sequence. The original Huse method performs this task on a distance matrix, whereas we do it based on the original sequences. The advantage of our approach is that the algorithm works on aligned sequences instead of a distance matrix. This is advantageous because by pre-clustering you remove a large number of sequences making the distance calculation much faster.
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62
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63 .. _pre.cluster: http://www.mothur.org/wiki/Pre.cluster
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64
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65 v1.24.0: Updated to mothur 1.33, added count and topdown parameter
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66 ]]>
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67 </help>
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68 <expand macro="citations"/>
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69 </tool>