Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.otus.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
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1 <tool id="mothur_get_otus" name="Get.otus" version="1.19.0"> |
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2 <description>Get otus containing sequences from specified groups</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='get.otus' |
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8 --outputdir='$logfile.extra_files_path' |
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9 --group=$group_in |
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10 --list=$list_in |
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11 --label=$label |
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12 #if $groupnames.source == 'groups': |
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13 #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0: |
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14 --groups=$groupnames.groups |
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15 #end if |
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16 #else |
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17 #if $groupnames.accnos.__str__ != "None" and len($groupnames.accnos.__str__) > 0: |
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18 --accnos=$groupnames.accnos |
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19 #end if |
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20 #end if |
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21 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
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22 #set results = $results + ["'" + $re.sub(r'^(.*)\.(.*?)',r'\1.pick.' + $label.__str__ + r'.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] |
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23 #set results = $results + ["'" + $re.sub(r'^(.*)\.(.*?)',r'\1.pick.'+ $label.__str__ + r'.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] |
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24 --result=#echo ','.join($results) |
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25 </command> |
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26 <inputs> |
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27 <param name="group_in" type="data" format="groups" label="group - Groups"/> |
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28 <param name="list_in" type="data" format="list" label="list - OTU List"/> |
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29 <param name="label" type="select" label="label - OTU Labels" > |
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30 <options> |
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31 <filter type="data_meta" ref="list_in" key="labels" /> |
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32 </options> |
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33 </param> |
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34 <conditional name="groupnames"> |
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35 <param name="source" type="select" label="Select Group Names from"> |
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36 <option value="groups">A List of Group Names</option> |
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37 <option value="accnos">A History Group Name Accnos Dataset</option> |
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38 </param> |
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39 <when value="groups"> |
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40 <param name="groups" type="select" label="groups - Pick groups to include" multiple="true" force_select="true"> |
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41 <help>At least one group must be selected</help> |
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42 <options> |
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43 <filter type="data_meta" ref="group_in" key="groups" /> |
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44 </options> |
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45 </param> |
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46 </when> |
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47 <when value="accnos"> |
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48 <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Group Names from your history"/> |
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49 </when> |
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50 </conditional> |
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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 ${on_string}: logfile" /> |
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54 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> |
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55 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/> |
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56 </outputs> |
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57 <requirements> |
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58 <requirement type="package" version="1.27">mothur</requirement> |
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59 </requirements> |
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60 <tests> |
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61 </tests> |
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62 <help> |
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63 **Mothur Overview** |
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64 |
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65 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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66 in the Department of Microbiology and Immunology at The University of Michigan, |
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67 provides bioinformatics for the microbial ecology community. |
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68 |
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69 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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70 |
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71 **Command Documenation** |
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72 |
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73 The get.otus_ command selects otus from a list_ containing sequences from a specific group or set of groups. |
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74 |
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75 .. _list: http://www.mothur.org/wiki/List_file |
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76 .. _get.otus: http://www.mothur.org/wiki/Get.otus |
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77 |
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78 |
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79 </help> |
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80 </tool> |