Mercurial > repos > iuc > mothur_otu_association
comparison otu.association.xml @ 2:3c42f300324e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:26:22 -0400 |
| parents | 4b4ca5a8e3e2 |
| children | 7cfe3ddd183a |
comparison
equal
deleted
inserted
replaced
| 1:435b52e38889 | 2:3c42f300324e |
|---|---|
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <expand macro="stdio"/> | 7 <expand macro="stdio"/> |
| 8 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
| 9 <command><![CDATA[ | 9 <command><![CDATA[ |
| 10 @SHELL_OPTIONS@ | 10 @SHELL_OPTIONS@ |
| 11 | 11 |
| 12 ## create symlinks to input datasets | 12 ## create symlinks to input datasets |
| 13 ln -s "$otu" otu.dat && | 13 ln -s '$otu' otu.dat && |
| 14 ln -s "$metadata" metadata.dat && | 14 ln -s '$metadata' metadata.dat && |
| 15 | 15 |
| 16 echo 'otu.association( | 16 echo 'otu.association( |
| 17 #if $otu.is_of_type("mothur.relabund"): | 17 #if $otu.is_of_type("mothur.relabund"): |
| 18 relabund=otu.dat | 18 relabund=otu.dat |
| 19 #elif $otu.is_of_type("mothur.shared"): | 19 #elif $otu.is_of_type("mothur.shared"): |
| 20 shared=otu.dat | 20 shared=otu.dat |
| 21 #end if | 21 #end if |
| 22 #if $label: | 22 #if $label: |
| 23 ,label=${ str($label).replace(",","-") } | 23 ,label=${ str($label).replace(",","-") } |
| 24 #end if | 24 #end if |
| 25 #if $groups: | 25 #if $groups: |
| 26 ,groups=${ str($groups).replace(",","-") } | 26 ,groups=${ str($groups).replace(",","-") } |
| 27 #end if | 27 #end if |
| 28 #if $method: | 28 #if $method: |
| 29 ,method=$method | 29 ,method=$method |
| 30 #end if | 30 #end if |
| 31 #if $metadata: | 31 #if $metadata: |
| 32 ,metadata=metadata.dat | 32 ,metadata=metadata.dat |
| 33 #end if | 33 #end if |
| 34 #if $cutoff: | 34 #if $cutoff: |
| 35 ,cutoff=$cutoff | 35 ,cutoff=$cutoff |
| 36 #end if | 36 #end if |
| 37 )' | 37 )' |
| 38 | sed 's/ //g' ## mothur trips over whitespace | 38 | sed 's/ //g' ## mothur trips over whitespace |
| 39 | mothur | 39 | mothur |
| 40 | tee mothur.out.log | 40 | tee mothur.out.log |
| 41 ]]></command> | 41 ]]></command> |
| 42 <inputs> | 42 <inputs> |
| 43 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/> | 43 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/> |
| 44 <param name="label" type="select" label="label - OTU Labels" multiple="true" help="By default all labels are used"> | 44 <param name="label" type="select" label="label - OTU Labels" multiple="true" help="By default all labels are used"> |
| 45 <expand macro="labeloptions"/> | 45 <expand macro="labeloptions"/> |
| 54 <option value="spearman">spearman</option> | 54 <option value="spearman">spearman</option> |
| 55 <option value="kendall">kendall</option> | 55 <option value="kendall">kendall</option> |
| 56 </param> | 56 </param> |
| 57 <param name="metadata" type="data" format="tabular" optional="true" label="metadata - find the association between the otus and the metadata."/> | 57 <param name="metadata" type="data" format="tabular" optional="true" label="metadata - find the association between the otus and the metadata."/> |
| 58 <param name="cutoff" type="float" value="" min="0" max="1" optional="true" label="cutoff - set a pvalue at which the otu will be reported"/> | 58 <param name="cutoff" type="float" value="" min="0" max="1" optional="true" label="cutoff - set a pvalue at which the otu will be reported"/> |
| 59 <expand macro="param-savelog"/> | |
| 59 </inputs> | 60 </inputs> |
| 60 <outputs> | 61 <outputs> |
| 61 <expand macro="logfile-output"/> | 62 <expand macro="logfile-output"/> |
| 62 <collection name="correlations" type="list" label="${tool.name} on ${on_string}: correlation coefficient files per OTU label"> | 63 <collection name="correlations" type="list" label="${tool.name} on ${on_string}: correlation coefficient files per OTU label"> |
| 63 <discover_datasets pattern=".*?\.(?P<designation>.*)\.otu\.corr" format="mothur.otu.corr"/> | 64 <discover_datasets pattern=".*?\.(?P<designation>.*)\.otu\.corr" format="mothur.otu.corr"/> |
| 67 <test><!-- test with shared file and default settings --> | 68 <test><!-- test with shared file and default settings --> |
| 68 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | 69 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> |
| 69 <output_collection name="correlations" count="36"> | 70 <output_collection name="correlations" count="36"> |
| 70 <element name="0.41.pearson" md5="ba93b529a7b0e5ca3baa8fe9a41b4107" ftype="mothur.otu.corr"/> | 71 <element name="0.41.pearson" md5="ba93b529a7b0e5ca3baa8fe9a41b4107" ftype="mothur.otu.corr"/> |
| 71 </output_collection> | 72 </output_collection> |
| 73 <param name="savelog" value="true"/> | |
| 72 <expand macro="logfile-test"/> | 74 <expand macro="logfile-test"/> |
| 73 </test> | 75 </test> |
| 74 <test><!-- test with relabund file and label and group select --> | 76 <test><!-- test with relabund file and label and group select --> |
| 75 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/> | 77 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/> |
| 76 <param name="method" value="kendall"/> | 78 <param name="method" value="kendall"/> |
| 77 <param name="label" value="0.03,0.05,0.36,0.41,0.55"/> | 79 <param name="label" value="0.03,0.05,0.36,0.41,0.55"/> |
| 78 <param name="groups" value="forest,pasture"/> | 80 <param name="groups" value="forest,pasture"/> |
| 79 <output_collection name="correlations" count="5"> | 81 <output_collection name="correlations" count="5"> |
| 80 <element name="0.41.kendall" md5="f01da5dc45d0bae35b692a7306bdc581" ftype="mothur.otu.corr"/> | 82 <element name="0.41.kendall" md5="f01da5dc45d0bae35b692a7306bdc581" ftype="mothur.otu.corr"/> |
| 81 </output_collection> | 83 </output_collection> |
| 84 <param name="savelog" value="true"/> | |
| 82 <expand macro="logfile-test"/> | 85 <expand macro="logfile-test"/> |
| 83 </test> | 86 </test> |
| 84 </tests> | 87 </tests> |
| 85 <help> | 88 <help><![CDATA[ |
| 86 <![CDATA[ | |
| 87 | 89 |
| 88 @MOTHUR_OVERVIEW@ | 90 @MOTHUR_OVERVIEW@ |
| 89 | 91 |
| 90 **Command Documentation** | 92 **Command Documentation** |
| 91 | 93 |
| 94 .. _shared: https://www.mothur.org/wiki/Shared_file | 96 .. _shared: https://www.mothur.org/wiki/Shared_file |
| 95 .. _relabund: https://www.mothur.org/wiki/Get.relabund | 97 .. _relabund: https://www.mothur.org/wiki/Get.relabund |
| 96 .. _otu.association: https://www.mothur.org/wiki/Otu.association | 98 .. _otu.association: https://www.mothur.org/wiki/Otu.association |
| 97 | 99 |
| 98 v.1.25.0: Updated to mothur 1.33, added cutoff option | 100 v.1.25.0: Updated to mothur 1.33, added cutoff option |
| 99 ]]> | 101 |
| 100 </help> | 102 ]]></help> |
| 101 <expand macro="citations"/> | 103 <expand macro="citations"/> |
| 102 </tool> | 104 </tool> |