Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.sabund.xml @ 27:49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 04 Dec 2012 11:05:19 -0600 |
parents | bfbaf823be4c |
children | 95d75b35e4d2 |
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1 <tool id="mothur_get_sabund" name="Get.sabund" version="1.19.0"> |
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2 <description>Get sabund from a otu list or rabund</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='get.sabund' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund |
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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, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): |
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11 --rabund=$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=$label |
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15 #end if |
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16 </command> |
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17 <inputs> |
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18 <param name="otu" type="data" format="list,rabund" label="list,rabund - List or Rabund"/> |
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19 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> |
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Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
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20 <options> |
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21 <filter type="data_meta" ref="otu" key="labels" /> |
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22 </options> |
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23 </param> |
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24 </inputs> |
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25 <outputs> |
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26 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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27 <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> |
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28 </outputs> |
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29 <requirements> |
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30 <requirement type="package" version="1.27">mothur</requirement> |
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31 </requirements> |
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32 <tests> |
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33 </tests> |
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34 <help> |
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35 **Mothur Overview** |
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36 |
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37 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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38 in the Department of Microbiology and Immunology at The University of Michigan, |
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39 provides bioinformatics for the microbial ecology community. |
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40 |
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41 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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42 |
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43 **Command Documenation** |
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44 |
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45 The get.sabund_ command generates an sabund_ file from a list_ or rabund_ file. |
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46 |
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47 .. _sabund: http://www.mothur.org/wiki/Sabund_file |
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48 .. _list: http://www.mothur.org/wiki/List_file |
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49 .. _rabund: http://www.mothur.org/wiki/Rabund_file |
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50 .. _get.sabund: http://www.mothur.org/wiki/Get.sabund |
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51 |
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52 |
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53 </help> |
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54 </tool> |