Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/create.database.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
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children | 95d75b35e4d2 |
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1 <tool id="mothur_create_database" name="Create.database" version="1.27.0" > |
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2 <description>creates a database file from a list, repnames, repfasta and contaxonomy file</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='create.database' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+?\.database$:'$database |
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7 --outputdir='$logfile.extra_files_path' |
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8 ## --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
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9 ## --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy','^\S+?\.(unique|[0-9.]*\.cons\.tax\.summary)$:tax.summary' |
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10 #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): |
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11 --shared=$otu |
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12 #else |
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13 --list=$otu |
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14 #end if |
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15 --repfasta=$repfasta |
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16 --repname=$repname |
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17 --contaxonomy=$contaxonomy |
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18 #if $label.__str__ != "None" and len($label.__str__) > 0: |
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19 --label='$label' |
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20 #end if |
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21 #if $group.__str__ != "None" and len($group.__str__) > 0: |
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22 --group='$group' |
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23 #end if |
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24 </command> |
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25 <inputs> |
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26 <param name="otu" type="data" format="list,shared" label="list or shared - OTU List of Shared"/> |
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27 <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta" |
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28 help="fasta file output by get.oturep"/> |
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29 <param name="repname" type="data" format="names" label="repname - rep.names" |
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30 help="names file output by get.oturep"/> |
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31 <param name="contaxonomy" type="select" format="cons.taxonomy" label="contaxonomy - Consensus Taxonomy" |
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32 help="consensus taxonomy file output by classify.otu"/> |
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33 <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/> |
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34 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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35 <options> |
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36 <filter type="data_meta" ref="otu" key="labels" /> |
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37 </options> |
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38 </param> |
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39 </inputs> |
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40 <outputs> |
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41 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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42 <data format="tabular" name="database" label="${tool.name} on ${on_string}: database" /> |
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43 </outputs> |
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44 <requirements> |
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45 <requirement type="package" version="1.27">mothur</requirement> |
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46 </requirements> |
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47 <tests> |
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48 </tests> |
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49 <help> |
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50 **Mothur Overview** |
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51 |
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52 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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53 in the Department of Microbiology and Immunology at The University of Michigan, |
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54 provides bioinformatics for the microbial ecology community. |
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55 |
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56 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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57 |
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58 **Command Documenation** |
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59 |
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60 The create.database_ command reads a list_ or shared_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file. |
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61 |
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62 .. _list: http://www.mothur.org/wiki/List_file |
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63 .. _shared: http://www.mothur.org/wiki/Shared_file |
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64 .. _create.database: http://www.mothur.org/wiki/Create.database |
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65 |
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66 |
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67 </help> |
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68 </tool> |