Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.rabund.xml @ 15:a6189f58fedb
Mothur - updated for Mothur version 1.22.0
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 08 Nov 2011 11:45:32 -0600 |
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children | bfbaf823be4c |
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1 <tool id="mothur_get_rabund" name="Get.rabund" version="1.19.0"> |
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2 <description>Get rabund from a otu list or sabund</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='get.rabund' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.rabund$:'$rabund |
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7 --outputdir='$logfile.extra_files_path' |
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8 #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): |
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9 --list=$otu |
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10 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__): |
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11 --sabund=$otu |
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12 #end if |
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13 #if $label.__str__ != "None" and len($label.__str__) > 0: |
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14 --label=$label |
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15 #end if |
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16 $sorted |
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17 </command> |
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18 <inputs> |
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19 <param name="otu" type="data" format="list,sabund" label="list,sabund - List or Sabund"/> |
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20 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> |
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21 <options from_dataset="otu"> |
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22 <column name="name" index="0"/> |
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23 <column name="value" index="0"/> |
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24 </options> |
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25 </param> |
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26 <param name="sorted" type="boolean" checked="false" truevalue="--sorted=true" falsevalue="" label="sorted - sort by abundance" |
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27 help="By default the data in the rabund file the same order as the OTUs in input, select to sort by abundance."/> |
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28 </inputs> |
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29 <outputs> |
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30 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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31 <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> |
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32 </outputs> |
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33 <requirements> |
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34 <requirement type="binary">mothur</requirement> |
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35 </requirements> |
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36 <tests> |
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37 </tests> |
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38 <help> |
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39 **Mothur Overview** |
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40 |
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41 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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42 in the Department of Microbiology and Immunology at The University of Michigan, |
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43 provides bioinformatics for the microbial ecology community. |
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44 |
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45 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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46 |
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47 **Command Documenation** |
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48 |
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49 The get.rabund_ command generates an rabund_ file from a list_ or sabund_ file. |
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50 |
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51 .. _rabund: http://www.mothur.org/wiki/Rabund_file |
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52 .. _list: http://www.mothur.org/wiki/List_file |
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53 .. _sabund: http://www.mothur.org/wiki/Sabund_file |
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54 .. _get.rabund: http://www.mothur.org/wiki/Get.rabund |
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55 |
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56 |
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57 </help> |
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58 </tool> |