Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/rarefaction.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 |
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1 <tool id="mothur_rarefaction_single" name="Rarefaction.single" version="1.19.0" force_history_refresh="True"> |
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2 <description>Generate intra-sample rarefaction 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='rarefaction.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='$__new_file_path__' |
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9 --new_datasets='^\S+?\.(((\S+)\.)?(rarefaction|r_\w*))$: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=$abund |
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27 #end if |
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28 #if int($iters.__str__) > 0: |
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29 --iters=$iters |
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30 #end if |
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31 #if float($freq.__str__) > 0: |
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32 --freq=$freq |
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33 #end if |
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34 --processors=2 |
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35 </command> |
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36 <inputs> |
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37 <param name="otu" type="data" format="list,rabund,sabund,shared" label="list,rabund,sabund,shared - OTU List"/> |
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38 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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39 <options from_dataset="otu"> |
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40 <column name="name" index="0"/> |
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41 <column name="value" index="0"/> |
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42 <filter type="unique_value" name="unq_lbl" column="0" /> |
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43 </options> |
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44 </param> |
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45 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> |
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46 <options from_file="mothur_calculators.loc"> |
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47 <column name="mult2" index="2"/> |
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48 <column name="name" index="0"/> |
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49 <column name="value" index="0"/> |
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50 <filter type="static_value" name="mult2" column="2" value="sing" /> |
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51 </options> |
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52 </param> |
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53 <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/> |
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54 <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/> |
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55 <param name="freq" type="float" value="0.0" label="freq - Reporting frequency" |
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56 help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/> |
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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 rarefaction.single_ command generates intra-sample rarefaction curves using a re-sampling without replacement approach. Rarefaction curves provide a way of comparing the richness observed in different samples. For calc parameter choices see: http://www.mothur.org/wiki/Calculators |
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78 |
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79 .. _rarefaction.single: http://www.mothur.org/wiki/Rarefaction.single |
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80 |
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81 </help> |
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82 </tool> |