Mercurial > repos > iuc > mothur_phylotype
comparison phylotype.xml @ 2:f750e0c2c7f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:17:49 -0400 |
| parents | 61cfe849101c |
| children | e6ecdb693d0c |
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| 1:e18d25fb125e | 2:f750e0c2c7f9 |
|---|---|
| 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 "$taxonomy" taxonomy.dat && | 13 ln -s '$taxonomy' taxonomy.dat && |
| 14 ln -s "$name" name.dat && | 14 ln -s '$name' name.dat && |
| 15 | 15 |
| 16 echo 'phylotype( | 16 echo 'phylotype( |
| 17 taxonomy=taxonomy.dat | 17 taxonomy=taxonomy.dat |
| 18 #if $cutoff: | 18 #if $cutoff: |
| 19 ,cutoff=$cutoff | 19 ,cutoff=$cutoff |
| 20 #end if | 20 #end if |
| 21 #if $name: | 21 #if $name: |
| 22 ,name=name.dat | 22 ,name=name.dat |
| 23 #end if | 23 #end if |
| 24 #if $label: | 24 #if $label: |
| 25 ,label=${ str($label).replace(",","-") } | 25 ,label=${ str($label).replace(",","-") } |
| 26 #end if | 26 #end if |
| 27 )' | 27 )' |
| 28 | sed 's/ //g' ## mothur trips over whitespace | 28 | sed 's/ //g' ## mothur trips over whitespace |
| 29 | mothur | 29 | mothur |
| 30 | tee mothur.out.log | 30 | tee mothur.out.log |
| 31 ]]></command> | 31 ]]></command> |
| 32 <inputs> | 32 <inputs> |
| 33 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/> | 33 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/> |
| 34 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names reference file for the taxonomy"/> | 34 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names reference file for the taxonomy"/> |
| 35 <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true"> | 35 <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true"> |
| 44 <option value="8">8</option> | 44 <option value="8">8</option> |
| 45 <option value="9">9</option> | 45 <option value="9">9</option> |
| 46 <option value="10">10</option> | 46 <option value="10">10</option> |
| 47 </param> | 47 </param> |
| 48 <param name="cutoff" type="integer" value="" min="0" max="50" optional="true" label="cutoff - Truncate the taxonomy at depth (Ignored if < 0)"/> | 48 <param name="cutoff" type="integer" value="" min="0" max="50" optional="true" label="cutoff - Truncate the taxonomy at depth (Ignored if < 0)"/> |
| 49 <expand macro="param-savelog"/> | |
| 49 </inputs> | 50 </inputs> |
| 50 <outputs> | 51 <outputs> |
| 51 <expand macro="logfile-output"/> | 52 <expand macro="logfile-output"/> |
| 52 <data name="rabund" format="mothur.rabund" from_work_dir="taxonomy*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> | 53 <data name="rabund" format="mothur.rabund" from_work_dir="taxonomy*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> |
| 53 <data name="sabund" format="mothur.sabund" from_work_dir="taxonomy*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> | 54 <data name="sabund" format="mothur.sabund" from_work_dir="taxonomy*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> |
| 57 <test> | 58 <test> |
| 58 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> | 59 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> |
| 59 <output name="rabund" md5="689fb6fd2fb4cd0740fc8b62d7e05556" ftype="mothur.rabund"/> | 60 <output name="rabund" md5="689fb6fd2fb4cd0740fc8b62d7e05556" ftype="mothur.rabund"/> |
| 60 <output name="sabund" md5="62547e84f1d051a16937715433f3d78a" ftype="mothur.sabund"/> | 61 <output name="sabund" md5="62547e84f1d051a16937715433f3d78a" ftype="mothur.sabund"/> |
| 61 <output name="otulist" md5="c808112d524863bbc973dd721ba18a06" ftype="mothur.list"/> | 62 <output name="otulist" md5="c808112d524863bbc973dd721ba18a06" ftype="mothur.list"/> |
| 63 <param name="savelog" value="true"/> | |
| 62 <expand macro="logfile-test"/> | 64 <expand macro="logfile-test"/> |
| 63 </test> | 65 </test> |
| 64 <test> | 66 <test> |
| 65 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> | 67 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> |
| 66 <param name="label" value="1,4,5"/> | 68 <param name="label" value="1,4,5"/> |
| 67 <param name="cutoff" value="5"/> | 69 <param name="cutoff" value="5"/> |
| 68 <output name="rabund" md5="3d2e3821bef6ecd7eaf0ea62e8692154" ftype="mothur.rabund"/> | 70 <output name="rabund" md5="3d2e3821bef6ecd7eaf0ea62e8692154" ftype="mothur.rabund"/> |
| 69 <output name="sabund" md5="582825c475bffbf7e450156ff26c844a" ftype="mothur.sabund"/> | 71 <output name="sabund" md5="582825c475bffbf7e450156ff26c844a" ftype="mothur.sabund"/> |
| 70 <output name="otulist" md5="424a2c62df2e37b32542731b9631f8ed" ftype="mothur.list"/> | 72 <output name="otulist" md5="424a2c62df2e37b32542731b9631f8ed" ftype="mothur.list"/> |
| 73 <param name="savelog" value="true"/> | |
| 71 <expand macro="logfile-test"/> | 74 <expand macro="logfile-test"/> |
| 72 </test> | 75 </test> |
| 73 </tests> | 76 </tests> |
| 74 <help> | 77 <help><![CDATA[ |
| 75 <![CDATA[ | |
| 76 | 78 |
| 77 @MOTHUR_OVERVIEW@ | 79 @MOTHUR_OVERVIEW@ |
| 78 | 80 |
| 79 **Command Documentation** | 81 **Command Documentation** |
| 80 | 82 |
| 83 .. _list: https://www.mothur.org/wiki/List_file | 85 .. _list: https://www.mothur.org/wiki/List_file |
| 84 .. _rabund: https://www.mothur.org/wiki/Rabund_file | 86 .. _rabund: https://www.mothur.org/wiki/Rabund_file |
| 85 .. _sabund: https://www.mothur.org/wiki/Sabund_file | 87 .. _sabund: https://www.mothur.org/wiki/Sabund_file |
| 86 .. _phylotype: https://www.mothur.org/wiki/Phylotype | 88 .. _phylotype: https://www.mothur.org/wiki/Phylotype |
| 87 | 89 |
| 88 ]]> | 90 ]]></help> |
| 89 </help> | |
| 90 <expand macro="citations"/> | 91 <expand macro="citations"/> |
| 91 </tool> | 92 </tool> |