Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/collect.single.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 |
parents | fcc0778f6987 |
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1 <tool id="mothur_collect_single" name="Collect.single" version="1.19.0" force_history_refresh="True"> |
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2 <description>Generate collector's curves for OTUs</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='collect.single' |
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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='$__new_file_path__' |
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9 --new_datasets='^\S+?\.(\S+)$:tabular' |
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10 #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): |
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11 --shared=$otu |
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12 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): |
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13 --rabund=$otu |
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14 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__): |
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15 --sabund=$otu |
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16 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): |
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17 --list=$otu |
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18 #end if |
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19 #if $label.__str__ != "None" and len($label.__str__) > 0: |
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20 --label='$label' |
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21 #end if |
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22 #if $calc.__str__ != "None" and len($calc.__str__) > 0: |
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23 --calc='$calc' |
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24 #end if |
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25 #if int($abund.__str__) > 0: |
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26 --abund=$abund |
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27 #end if |
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28 #if int($size.__str__) > 0: |
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29 --size=$size |
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30 #end if |
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31 #if float($freq.__str__) > 0: |
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32 --freq=$freq |
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33 #end if |
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34 </command> |
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35 <inputs> |
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36 <param name="otu" type="data" format="list,rabund,sabund,shared" label="list,rabund,sabund,shared - OTU List"/> |
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37 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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38 <options from_dataset="otu"> |
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39 <column name="name" index="0"/> |
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40 <column name="value" index="0"/> |
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41 <filter type="unique_value" name="unq_lbl" column="0" /> |
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42 </options> |
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43 </param> |
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44 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> |
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45 <options from_file="mothur_calculators.loc"> |
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46 <column name="mult" index="1"/> |
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47 <column name="name" index="0"/> |
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48 <column name="value" index="0"/> |
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49 <filter type="static_value" name="mult" column="1" value="single" /> |
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50 </options> |
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51 </param> |
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52 <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs (default 10)"/> |
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53 <param name="size" type="integer" value="0" label="size - sample size for OTU prediction (ignored if < 1)" |
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54 help="By default these calculators will base the prediction on a sample that is the same size as the initial sampling"/> |
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55 <param name="freq" type="float" value="0.0" label="freq - frequency for output (default is every 100 sequences)" |
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56 help="Use a decimal between 0 and 1 to set the frequency as a percentage of the number of sequences"/> |
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57 </inputs> |
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58 <outputs> |
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59 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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60 </outputs> |
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61 <requirements> |
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62 <requirement type="binary">mothur</requirement> |
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63 </requirements> |
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64 <tests> |
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65 </tests> |
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66 <help> |
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67 **Mothur Overview** |
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68 |
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69 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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70 in the Department of Microbiology and Immunology at The University of Michigan, |
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71 provides bioinformatics for the microbial ecology community. |
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72 |
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73 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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74 |
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75 **Command Documenation** |
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76 |
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77 The collect.single_ command generates collector's curves using calculators_, that describe the richness, diversity, and other features of individual samples. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. Otherwise, you need to keep sampling. For calc parameter choices see: http://www.mothur.org/wiki/Calculators |
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78 |
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79 .. _calculators: http://www.mothur.org/wiki/Calculators |
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80 .. _collect.single: http://www.mothur.org/wiki/Collect.single |
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81 |
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82 </help> |
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83 </tool> |