Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/pca.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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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1 <tool id="mothur_pca" name="Pca" version="1.19.0"> |
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2 <description>Principal Coordinate Analysis for a shared file</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 ## 98_sq_phylip_amazon.fn.unique.pca.axes |
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6 ## 98_sq_phylip_amazon.fn.unique.pca.loadings |
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7 --cmd='pca' |
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8 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pca.axes$:'$pca_axes,'^\S+\.pca.loadings$:'$pca_loadings |
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9 --outputdir='$logfile.extra_files_path' |
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10 #if isinstance($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, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__): |
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13 --relabund=$otu |
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14 #end if |
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15 #if $label.__str__ != "None" and len($label.__str__) > 0: |
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16 --label='$label' |
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17 #end if |
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18 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
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19 --groups='$groups' |
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20 #end if |
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21 $metric |
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22 </command> |
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23 <inputs> |
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24 <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/> |
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25 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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26 <options from_dataset="otu"> |
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27 <column name="name" index="0"/> |
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28 <column name="value" index="0"/> |
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29 <filter type="unique_value" name="unq_lbl" column="0" /> |
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30 </options> |
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31 </param> |
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32 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> |
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33 <options from_dataset="otu"> |
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34 <column name="name" index="1"/> |
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35 <column name="value" index="1"/> |
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36 <filter type="unique_value" name="unq_grp" column="1" /> |
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37 </options> |
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38 </param> |
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39 <param name="metric" type="boolean" truevalue="" falsevalue="--metric=False" checked="true" label="metric - Calculate pearson correlation coefficient" /> |
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40 </inputs> |
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41 <outputs> |
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42 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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43 <data format="axes" name="pca_axes" label="${tool.name} on ${on_string}: pca.axes" /> |
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44 <data format="txt" name="pca_loadings" label="${tool.name} on ${on_string}: pca.loadings" /> |
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45 </outputs> |
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46 <requirements> |
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47 <requirement type="binary">mothur</requirement> |
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48 </requirements> |
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49 <tests> |
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50 </tests> |
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51 <help> |
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52 **Mothur Overview** |
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53 |
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54 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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55 in the Department of Microbiology and Immunology at The University of Michigan, |
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56 provides bioinformatics for the microbial ecology community. |
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57 |
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58 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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59 |
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60 **Command Documenation** |
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61 |
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62 The pca_ command generate principle components plot data for a shared_ or relabund_ file. |
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63 |
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64 .. _shared: http://www.mothur.org/wiki/Shared_file |
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65 .. _relabund: http://www.mothur.org/wiki/Get.relabund |
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66 .. _pca: http://www.mothur.org/wiki/Pca |
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67 |
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68 </help> |
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69 </tool> |