Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/parse.list.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
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date | Mon, 10 Nov 2014 15:40:02 -0500 |
parents | 95d75b35e4d2 |
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1 <tool id="mothur_parse_list" name="Parse.list" version="1.19.0" force_history_refresh="True"> |
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2 <description>Generate a List file for each group</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='parse.list' |
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6 --result='^mothur.\S+\.logfile$:'$logfile |
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7 --outputdir='$logfile.extra_files_path' |
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8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
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9 --new_datasets='^\S+?\.(\S+\.list)$:list' |
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10 --list=$otu |
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11 --group=$group |
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12 #if $label.__str__ != "None" and len($label.__str__) > 0: |
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13 --label='$label' |
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14 #end if |
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15 #if $count.__str__ != "None" and len($count.__str__) > 0: |
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16 --count=$count |
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17 #end if |
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18 </command> |
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19 <inputs> |
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20 <param name="otu" type="data" format="list" label="list - OTU List"/> |
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21 <param name="group" type="data" format="groups" label="group - Sequences Name reference"/> |
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22 <param name="label" type="select" optional="true" label="label - To filter: Select OTU Labels to include" multiple="true"> |
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23 <help>All labels are included if none are selected</help> |
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24 <options> |
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25 <filter type="data_meta" ref="otu" key="labels" /> |
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26 </options> |
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27 </param> |
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28 <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> |
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29 </inputs> |
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30 <outputs> |
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31 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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32 </outputs> |
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33 <requirements> |
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34 <requirement type = "package" version ="1.33">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 parse.list_ command reads a list_ file and group_ file and generates a list_ file for each group_ in the groupfile. |
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50 |
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51 .. _list: http://www.mothur.org/wiki/List_file |
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52 .. _group: http://www.mothur.org/wiki/Group_file |
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53 .. _parse.list: http://www.mothur.org/wiki/Parse.list |
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54 |
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55 v.1.19.0: Updated to mothur 1.33, added count parameter |
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56 |
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57 </help> |
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58 </tool> |