Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/otu.hierarchy.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
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children | 370b3fc4e7d3 |
rev | line source |
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2
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1 <tool id="mothur_otu_hierarchy" name="Otu.hierarchy" version="1.19.0"> |
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2 <description>Relate OTUs at different distances</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 ## output {group_file_name}.pick.{label}.groups {list_file_name}.pick.{label}.list |
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6 #import re, os.path |
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7 --cmd='otu.hierarchy' |
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8 --outputdir='$logfile.extra_files_path' |
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9 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.otu\.hierarchy$:'$hierarchy |
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10 --list=$list |
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11 --label=$label1,$label2 |
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12 --output=$output |
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13 </command> |
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14 <inputs> |
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15 <param name="list" type="data" format="list" label="list - OTU List"/> |
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16 <param name="label1" type="select" label="label - OTU Label 1" > |
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17 <options from_dataset="list"> |
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18 <column name="name" index="0"/> |
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19 <column name="value" index="0"/> |
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20 </options> |
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21 </param> |
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22 <param name="label2" type="select" label="label - OTU Label 2" help="Must be different than Label 1"> |
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23 <options from_dataset="list"> |
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24 <column name="name" index="0"/> |
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25 <column name="value" index="0"/> |
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26 <filter type="param_value" ref="label1" column="value" keep="false"/> |
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27 </options> |
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28 </param> |
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29 <param name="output" type="select" optional="true" label="output - display the names of the sequences in the otus or the otu numbers"> |
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30 <option value="name" selected="treu">OTU sequence names</option> |
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31 <option value="number">OTU numbers</option> |
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32 </param> |
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33 </inputs> |
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34 <outputs> |
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35 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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36 <data format="tabular" name="hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/> |
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37 </outputs> |
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38 <requirements> |
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39 <requirement type="binary">mothur</requirement> |
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40 </requirements> |
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41 <tests> |
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42 </tests> |
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43 <help> |
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44 **Mothur Overview** |
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45 |
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46 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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47 in the Department of Microbiology and Immunology at The University of Michigan, |
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48 provides bioinformatics for the microbial ecology community. |
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49 |
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50 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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51 |
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52 **Command Documenation** |
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53 |
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54 The otu.hierarchy_ command relates OTUs from a list_ at different distances. |
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55 |
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56 .. _list_file: http://www.mothur.org/wiki/List_file |
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57 .. _otu.hierarchy: http://www.mothur.org/wiki/Otu.hierarchy |
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58 |
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59 |
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60 </help> |
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61 </tool> |