Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/make.shared.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_make_shared" name="Make.shared" version="1.23.0" force_history_refresh="True"> |
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2 <description>Make a shared file from a list and a group</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 #import re, os.path |
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6 --cmd='make.shared' |
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7 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared$:'$shared |
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8 --outputdir='$logfile.extra_files_path' |
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9 #if $as_datasets.__str__ == "yes": |
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10 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
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11 --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund' |
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12 #end if |
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13 --list=$list |
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14 |
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15 #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('groups').__class__): |
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16 --group=$group |
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17 #else: |
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18 --count=$group |
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19 #end if |
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20 |
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21 #if $label.__str__ != "None" and len($label.__str__) > 0: |
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22 --label='$label' |
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23 #end if |
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24 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
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25 --groups=$groups |
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26 #end if |
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27 #* |
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28 #if $ordergroup.__str__ != "None" and len($ordergroup.__str__) > 0: |
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29 --ordergroup=$ordergroup |
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30 #end if |
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31 *# |
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32 </command> |
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33 <inputs> |
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34 <param name="list" type="data" format="list" label="list - OTU List"/> |
35
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35 <param name="group" type="data" format="groups, count" label="group - "/> |
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36 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" |
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37 help="By default all are included if no selection is made."> |
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38 <options> |
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39 <filter type="data_meta" ref="list" key="labels" /> |
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40 </options> |
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41 </param> |
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42 <param name="groups" type="select" label="groups - Groups to include" multiple="true"> |
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43 <options> |
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44 <filter type="data_meta" ref="group" key="groups" /> |
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45 </options> |
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46 </param> |
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47 <!-- |
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48 <param name="ordergroup" type="data" format="groups" optional="true" label="ordergroup - one column list of group names in desired order"/> |
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49 --> |
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50 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each group rabund"/> |
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51 </inputs> |
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52 <outputs> |
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53 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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54 <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" /> |
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55 </outputs> |
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56 <requirements> |
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57 <requirement type="package" version="1.33">mothur</requirement> |
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58 </requirements> |
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59 <tests> |
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60 </tests> |
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61 <help> |
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62 **Mothur Overview** |
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63 |
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64 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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65 in the Department of Microbiology and Immunology at The University of Michigan, |
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66 provides bioinformatics for the microbial ecology community. |
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67 |
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68 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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69 |
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70 **Command Documenation** |
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71 |
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72 The make.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group. |
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73 |
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74 |
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75 .. _list: http://www.mothur.org/wiki/List_file |
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76 .. _group: http://www.mothur.org/wiki/Group_file |
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77 .. _shared: http://www.mothur.org/wiki/Shared_file |
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78 .. _rabund: http://www.mothur.org/wiki/Rabund_file |
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79 .. _make.shared: http://www.mothur.org/wiki/Make.shared |
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80 |
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81 </help> |
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82 </tool> |