Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/phylo.diversity.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_phylo_diversity" name="Phylo.diversity" version="1.19.0"> |
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2 <description>Alpha Diversity calculates unique branch length</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='phylo.diversity' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.phylodiv\.summary$:'$summary_out,'^\S+\.phylodiv$:'$collectors_out,'^\S+\.rarefaction$:'$rarefaction_out |
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7 --outputdir='$logfile.extra_files_path' |
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8 --tree=$tree |
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9 #if $group.__str__ != "None" and len($group.__str__) > 0: |
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10 --group='$group' |
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11 #end if |
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12 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
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13 --groups='$groups' |
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14 #end if |
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15 #if $name.__str__ != "None" and len($name.__str__) > 0: |
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16 --name='$name' |
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17 #end if |
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18 #if int($iters.__str__) > 0: |
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19 --iters=$iters |
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20 #end if |
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21 #if float($freq.__str__) > 0: |
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22 --freq=$freq |
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23 #end if |
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24 $scale |
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25 $collect |
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26 $rarefy |
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27 #if len($rarefy.__str__) > 0 or len($collect.__str__) > 0: |
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28 $summary |
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29 #end if |
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30 --processors=2 |
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31 </command> |
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32 <inputs> |
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33 <!-- list,group or shared --> |
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34 <param name="tree" type="data" format="tre" label="tree - Phylogenetic Tree"/> |
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35 <param name="group" type="data" format="groups" label="group - Group file for the tree"/> |
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36 <param name="groups" type="select" label="groups - Groups to display" multiple="true"> |
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37 <options from_dataset="group"> |
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38 <column name="name" index="1"/> |
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39 <column name="value" index="1"/> |
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40 <filter type="unique_value" name="unq_grp" column="1" /> |
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41 </options> |
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42 </param> |
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43 <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file for the tree"/> |
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44 <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/> |
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45 <param name="freq" type="float" value="0.0" label="freq - Reporting frequency" |
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46 help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/> |
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47 |
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48 <param name="scale" type="boolean" truevalue="--scale=true" falsevalue="" checked="false" label="scale - Scale output to the number of sequences sampled" /> |
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49 <param name="rarefy" type="boolean" truevalue="--rarefy=true" falsevalue="" checked="false" label="rarefy - Calculate the rarefaction data" /> |
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50 <param name="summary" type="boolean" truevalue="" falsevalue="--summary=false" checked="true" label="summary - Generate a summary file" /> |
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51 <param name="collect" type="boolean" truevalue="--collect=true" falsevalue="" checked="false" label="collect - Create a collectors curve" /> |
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52 </inputs> |
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53 <outputs> |
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54 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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55 <data format="tabular" name="summary_out" label="${tool.name} on ${on_string}: summary"> |
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56 <filter>summary == True</filter> |
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57 </data> |
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58 <data format="tabular" name="rarefaction_out" label="${tool.name} on ${on_string}: rarefaction"> |
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59 <filter>rarefy == True</filter> |
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60 </data> |
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61 <data format="tabular" name="collectors_out" label="${tool.name} on ${on_string}: collectors"> |
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62 <filter>collect == True</filter> |
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63 </data> |
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64 <!-- random uses input prompts, not sure how to model that |
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65 <data format="tabular" name="random" label="${tool.name} on ${on_string}: random"> |
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66 </data> |
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67 --> |
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68 </outputs> |
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69 <requirements> |
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70 <requirement type="binary">mothur</requirement> |
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71 </requirements> |
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72 <tests> |
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73 </tests> |
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74 <help> |
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75 **Mothur Overview** |
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76 |
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77 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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78 in the Department of Microbiology and Immunology at The University of Michigan, |
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79 provides bioinformatics for the microbial ecology community. |
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80 |
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81 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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82 |
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83 **Command Documenation** |
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84 |
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85 The phylo.diversity_ command calculates alpha diversity as the total of the unique branch length. |
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86 |
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87 .. _phylo.diversity: http://www.mothur.org/wiki/Phylo.diversity |
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88 |
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89 |
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90 </help> |
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91 </tool> |