Mercurial > repos > iuc > mothur_create_database
comparison create.database.xml @ 2:024a52bdf70c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 21:54:19 -0400 |
| parents | 9ab5ebae3fb2 |
| children |
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| 1:57fba40a8d96 | 2:024a52bdf70c |
|---|---|
| 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 "$repfasta" repfasta.dat && | 14 ln -s '$repfasta' repfasta.dat && |
| 15 ln -s "$nameOrCount" nameOrCount.dat && | 15 ln -s '$nameOrCount' nameOrCount.dat && |
| 16 ln -s "$constaxonomy" constaxonomy.dat && | 16 ln -s '$constaxonomy' constaxonomy.dat && |
| 17 ln -s "$group" group.dat && | 17 ln -s '$group' group.dat && |
| 18 | 18 |
| 19 echo 'create.database( | 19 echo 'create.database( |
| 20 #if $otu.is_of_type("mothur.list"): | 20 #if $otu.is_of_type("mothur.list"): |
| 21 list=otu.dat | 21 list=otu.dat |
| 22 #elif $otu.is_of_type("mothur.shared"): | 22 #elif $otu.is_of_type("mothur.shared"): |
| 23 shared=otu.dat | 23 shared=otu.dat |
| 24 #end if | 24 #end if |
| 25 ,repfasta=repfasta.dat | 25 ,repfasta=repfasta.dat |
| 26 #if $nameOrCount.is_of_type("mothur.names"): | 26 #if $nameOrCount.is_of_type("mothur.names"): |
| 27 ,repname=nameOrCount.dat | 27 ,repname=nameOrCount.dat |
| 28 #elif $nameOrCount.is_of_type("mothur.count_table"): | 28 #elif $nameOrCount.is_of_type("mothur.count_table"): |
| 29 ,count=nameOrCount.dat | 29 ,count=nameOrCount.dat |
| 30 #end if | 30 #end if |
| 31 ,constaxonomy=constaxonomy.dat | 31 ,constaxonomy=constaxonomy.dat |
| 32 #if $group: | 32 #if $group: |
| 33 ,group=group.dat | 33 ,group=group.dat |
| 34 #end if | 34 #end if |
| 35 #if $label: | 35 #if $label: |
| 36 ,label=$label | 36 ,label=$label |
| 37 #end if | 37 #end if |
| 38 )' | 38 )' |
| 39 | sed 's/ //g' ## mothur trips over whitespace | 39 | sed 's/ //g' ## mothur trips over whitespace |
| 40 | mothur | 40 | mothur |
| 41 | tee mothur.out.log | 41 | tee mothur.out.log |
| 42 ]]></command> | 42 ]]></command> |
| 43 <inputs> | 43 <inputs> |
| 44 <param name="otu" type="data" format="mothur.list,mothur.shared" label="list or shared - OTU List of Shared"/> | 44 <param name="otu" type="data" format="mothur.list,mothur.shared" label="list or shared - OTU List of Shared"/> |
| 45 <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta" help="rep.fasta file generated by get.oturep"/> | 45 <param name="repfasta" type="data" format="fasta" optional="true" label="repfasta - rep.fasta" help="rep.fasta file generated by get.oturep"/> |
| 46 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="repname/count - Representative sequences" help="rep.name file or rep.count_table file generated by get.oturep"/> | 46 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" optional="true" label="repname/count - Representative sequences" |
| 47 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy" help="consensus taxonomy file output by classify.otu"/> | 47 help="rep.name file or rep.count_table file generated by get.oturep"/> |
| 48 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy" | |
| 49 help="consensus taxonomy file output by classify.otu"/> | |
| 48 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/> | 50 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/> |
| 49 <param name="label" type="select" label="label - OTU Labels" optional="true" help="Select exactly one label. If none selected, first label in your list or shared file will be used"> | 51 <param name="label" type="select" label="label - OTU Labels" optional="true" |
| 52 help="Select exactly one label. If none selected, first label in your list or shared file will be used"> | |
| 50 <expand macro="labeloptions"/> | 53 <expand macro="labeloptions"/> |
| 51 </param> | 54 </param> |
| 55 <expand macro="param-savelog"/> | |
| 52 </inputs> | 56 </inputs> |
| 53 <outputs> | 57 <outputs> |
| 54 <expand macro="logfile-output"/> | 58 <expand macro="logfile-output"/> |
| 55 <data name="database" format="tabular" from_work_dir="otu*.database" label="${tool.name} on ${on_string}: database"/> | 59 <data name="database" format="tabular" from_work_dir="otu*.database" label="${tool.name} on ${on_string}: database"/> |
| 56 </outputs> | 60 </outputs> |
| 61 <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/> | 65 <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/> |
| 62 <param name="nameOrCount" value="cd-test.repname" ftype="mothur.names"/> | 66 <param name="nameOrCount" value="cd-test.repname" ftype="mothur.names"/> |
| 63 <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/> | 67 <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/> |
| 64 <param name="label" value="unique"/> | 68 <param name="label" value="unique"/> |
| 65 <output name="database" file="cd-test.database" ftype="tabular"/> | 69 <output name="database" file="cd-test.database" ftype="tabular"/> |
| 70 <param name="savelog" value="true"/> | |
| 66 <expand macro="logfile-test"/> | 71 <expand macro="logfile-test"/> |
| 67 </test> | 72 </test> |
| 68 <!-- Test with a mothur.count_table file --> | 73 <!-- Test with a mothur.count_table file --> |
| 69 <test> | 74 <test> |
| 70 <param name="otu" value="cd-test.list" ftype="mothur.list"/> | 75 <param name="otu" value="cd-test.list" ftype="mothur.list"/> |
| 71 <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/> | 76 <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/> |
| 72 <param name="nameOrCount" value="cd-test.count_table" ftype="mothur.count_table"/> | 77 <param name="nameOrCount" value="cd-test.count_table" ftype="mothur.count_table"/> |
| 73 <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/> | 78 <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/> |
| 74 <param name="label" value="unique"/> | 79 <param name="label" value="unique"/> |
| 75 <output name="database" file="cd-test.database" ftype="tabular"/> | 80 <output name="database" file="cd-test.database" ftype="tabular"/> |
| 81 <param name="savelog" value="true"/> | |
| 76 <expand macro="logfile-test"/> | 82 <expand macro="logfile-test"/> |
| 77 </test> | 83 </test> |
| 78 </tests> | 84 </tests> |
| 79 <help> | 85 <help><![CDATA[ |
| 80 <![CDATA[ | |
| 81 | 86 |
| 82 @MOTHUR_OVERVIEW@ | 87 @MOTHUR_OVERVIEW@ |
| 83 | 88 |
| 84 **Command Documentation** | 89 **Command Documentation** |
| 85 | 90 |
| 89 .. _shared: https://www.mothur.org/wiki/Shared_file | 94 .. _shared: https://www.mothur.org/wiki/Shared_file |
| 90 .. _create.database: https://www.mothur.org/wiki/Create.database | 95 .. _create.database: https://www.mothur.org/wiki/Create.database |
| 91 | 96 |
| 92 v.1.28.0: Updated to Mothur 1.33, added count paramter. | 97 v.1.28.0: Updated to Mothur 1.33, added count paramter. |
| 93 | 98 |
| 94 ]]> | 99 ]]></help> |
| 95 </help> | |
| 96 <expand macro="citations"/> | 100 <expand macro="citations"/> |
| 97 </tool> | 101 </tool> |