Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/summary.tax.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 |
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1 <tool id="mothur_summary_tax" name="Summary.tax" version="1.23.0"> |
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2 <description>Assign sequences to taxonomy</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='summary.tax' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tax\.summary$:'$tax_summary |
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7 --outputdir='$logfile.extra_files_path' |
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8 --taxonomy=$tax.taxonomy |
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9 #if $name.__str__ != "None" and len($name.__str__) > 0: |
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10 --name='$name' |
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11 #end if |
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12 #if $group.__str__ != "None" and len($group.__str__) > 0: |
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13 --group='$group' |
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14 #end if |
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15 #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0: |
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16 --reftaxonomy=$reftax.taxonomy |
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17 #end if |
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18 #if $count.__str__ != "None" and len($count.__str__) > 0: |
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19 --count=$count |
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20 #end if |
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21 $relabund |
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22 </command> |
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23 <inputs> |
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24 <conditional name="tax"> |
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25 <param name="source" type="select" label="Select Taxonomy from" help=""> |
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26 <option value="hist">History</option> |
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27 <option value="ref">Cached Reference</option> |
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28 </param> |
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29 <when value="ref"> |
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30 <param name="taxonomy" type="select" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"> |
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31 <options from_data_table="mothur_taxonomy"> |
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32 </options> |
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33 </param> |
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34 </when> |
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35 <when value="hist"> |
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36 <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"/> |
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37 </when> |
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38 </conditional> |
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39 <param name="name" type="data" format="names" optional="true" label="name - taxonomy sequence names"/> |
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40 <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/> |
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41 <conditional name="reftax"> |
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42 <param name="source" type="select" label="Select Reference Taxonomy used in Summary.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static."> |
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43 <option value="none">Selection is Optional</option> |
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44 <option value="hist">History</option> |
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45 <option value="ref">Cached Reference</option> |
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46 </param> |
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47 <when value="none"/> |
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48 <when value="ref"> |
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49 <param name="taxonomy" type="select" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"> |
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50 <options from_data_table="mothur_taxonomy"> |
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51 </options> |
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52 </param> |
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53 </when> |
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54 <when value="hist"> |
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55 <param name="taxonomy" type="data" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/> |
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56 </when> |
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57 </conditional> |
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58 <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> |
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59 <param name="relabund" type="boolean" falsevalue="" truevalue="--relabund=true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/> |
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60 </inputs> |
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61 <outputs> |
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62 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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63 <data format="summary" name="tax_summary" label="${tool.name} on ${on_string}: summary" /> |
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64 </outputs> |
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65 <requirements> |
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66 <requirement type = "package" version ="1.33">mothur</requirement> |
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67 </requirements> |
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68 <tests> |
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69 </tests> |
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70 <help> |
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71 **Mothur Overview** |
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72 |
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73 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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74 in the Department of Microbiology and Immunology at The University of Michigan, |
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75 provides bioinformatics for the microbial ecology community. |
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76 |
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77 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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78 |
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79 **Command Documenation** |
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80 |
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81 The summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information. |
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82 |
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83 .. _summary.tax: http://www.mothur.org/wiki/Summary.otu |
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84 |
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85 </help> |
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86 </tool> |