Mercurial > repos > iuc > mothur_get_sabund
comparison get.sabund.xml @ 2:502c0ba699fb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:27:36 -0400 |
| parents | 579ffc8e2b4b |
| children |
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| 1:73eb41b03dfd | 2:502c0ba699fb |
|---|---|
| 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 "$count" count.dat && | 14 ln -s '$count' count.dat && |
| 15 | 15 |
| 16 echo 'get.sabund( | 16 echo 'get.sabund( |
| 17 #if $label: | 17 #if $label: |
| 18 label=${ str($label).replace(",","-") }, | 18 label=${ str($label).replace(",","-") }, |
| 19 #end if | 19 #end if |
| 20 #if $count: | 20 #if $count: |
| 21 count=count.dat, | 21 count=count.dat, |
| 22 #end if | 22 #end if |
| 23 #if $otu.is_of_type("mothur.list"): | 23 #if $otu.is_of_type("mothur.list"): |
| 24 list=otu.dat | 24 list=otu.dat |
| 25 #elif $otu.is_of_type("mothur.rabund"): | 25 #elif $otu.is_of_type("mothur.rabund"): |
| 26 rabund=otu.dat | 26 rabund=otu.dat |
| 27 #end if | 27 #end if |
| 28 )' | 28 )' |
| 29 | sed 's/ //g' ## mothur trips over whitespace | 29 | sed 's/ //g' ## mothur trips over whitespace |
| 30 | mothur | 30 | mothur |
| 31 | tee mothur.out.log | 31 | tee mothur.out.log |
| 32 ]]></command> | 32 ]]></command> |
| 33 <inputs> | 33 <inputs> |
| 34 <param name="otu" type="data" format="mothur.list,mothur.rabund" label="list,rabund - List or Rabund"/> | 34 <param name="otu" type="data" format="mothur.list,mothur.rabund" label="list,rabund - List or Rabund"/> |
| 35 <param name="label" type="select" optional="true" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> | 35 <param name="label" type="select" optional="true" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> |
| 36 <expand macro="labeloptions"/> | 36 <expand macro="labeloptions"/> |
| 37 </param> | 37 </param> |
| 38 <param name="count" type="data" format="mothur.count_table" optional="true" help="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/> | 38 <param name="count" type="data" format="mothur.count_table" optional="true" |
| 39 help="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/> | |
| 40 <expand macro="param-savelog"/> | |
| 39 </inputs> | 41 </inputs> |
| 40 <outputs> | 42 <outputs> |
| 41 <expand macro="logfile-output"/> | 43 <expand macro="logfile-output"/> |
| 42 <data name="sabund" format="mothur.sabund" from_work_dir="otu*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> | 44 <data name="sabund" format="mothur.sabund" from_work_dir="otu*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> |
| 43 </outputs> | 45 </outputs> |
| 44 <tests> | 46 <tests> |
| 45 <test><!-- test rabund input --> | 47 <test><!-- test rabund input --> |
| 46 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/> | 48 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/> |
| 47 <output name="sabund" file="amazon.an.sabund2" ftype="mothur.sabund"/> | 49 <output name="sabund" file="amazon.an.sabund2" ftype="mothur.sabund"/> |
| 50 <param name="savelog" value="true"/> | |
| 48 <expand macro="logfile-test"/> | 51 <expand macro="logfile-test"/> |
| 49 </test> | 52 </test> |
| 50 <test><!-- test otu list input --> | 53 <test><!-- test otu list input --> |
| 51 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> | 54 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> |
| 52 <param name="label" value="0.03,0.05"/> | 55 <param name="label" value="0.03,0.05"/> |
| 53 <output name="sabund" file="amazon.an.sabund3" ftype="mothur.sabund"/> | 56 <output name="sabund" file="amazon.an.sabund3" ftype="mothur.sabund"/> |
| 57 <param name="savelog" value="true"/> | |
| 54 <expand macro="logfile-test"/> | 58 <expand macro="logfile-test"/> |
| 55 </test> | 59 </test> |
| 56 </tests> | 60 </tests> |
| 57 <help> | 61 <help><![CDATA[ |
| 58 <![CDATA[ | |
| 59 | 62 |
| 60 @MOTHUR_OVERVIEW@ | 63 @MOTHUR_OVERVIEW@ |
| 61 | 64 |
| 62 | 65 |
| 63 **Command Documentation** | 66 **Command Documentation** |
| 67 .. _sabund: https://www.mothur.org/wiki/Sabund_file | 70 .. _sabund: https://www.mothur.org/wiki/Sabund_file |
| 68 .. _list: https://www.mothur.org/wiki/List_file | 71 .. _list: https://www.mothur.org/wiki/List_file |
| 69 .. _rabund: https://www.mothur.org/wiki/Rabund_file | 72 .. _rabund: https://www.mothur.org/wiki/Rabund_file |
| 70 .. _get.sabund: https://www.mothur.org/wiki/Get.sabund | 73 .. _get.sabund: https://www.mothur.org/wiki/Get.sabund |
| 71 | 74 |
| 72 ]]> | 75 ]]></help> |
| 73 </help> | |
| 74 <expand macro="citations"/> | 76 <expand macro="citations"/> |
| 75 </tool> | 77 </tool> |