Mercurial > repos > iuc > mothur_deunique_seqs
comparison deunique.seqs.xml @ 2:3291237294fe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:14:50 -0400 |
| parents | 4b2dabf45996 |
| children | 3767f899f13c |
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| 1:127484a400e7 | 2:3291237294fe |
|---|---|
| 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 "$fasta" fasta.dat && | 13 ln -s '$fasta' fasta.dat && |
| 14 ln -s "$names" names.dat && | 14 ln -s '$names' names.dat && |
| 15 | 15 |
| 16 echo 'deunique.seqs( | 16 echo 'deunique.seqs( |
| 17 #if $inputtype.intype == "countfile": | 17 #if $inputtype.intype == "countfile": |
| 18 count=names.dat, | 18 count=names.dat, |
| 19 #else | 19 #else |
| 20 name=names.dat, | 20 name=names.dat, |
| 21 #end if | 21 #end if |
| 22 fasta=fasta.dat | 22 fasta=fasta.dat |
| 23 )' | 23 )' |
| 24 | sed 's/ //g' ## mothur trips over whitespace | 24 | sed 's/ //g' ## mothur trips over whitespace |
| 25 | mothur | 25 | mothur |
| 26 | tee mothur.out.log | 26 | tee mothur.out.log |
| 27 ]]></command> | 27 ]]></command> |
| 28 <inputs> | 28 <inputs> |
| 29 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> | 29 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> |
| 30 <conditional name="inputtype"> | 30 <conditional name="inputtype"> |
| 31 <param name="intype" type="select" label="type of file to provide, may be either a names or a count file" help=""> | 31 <param name="intype" type="select" label="type of file to provide, may be either a names or a count file" help=""> |
| 34 </param> | 34 </param> |
| 35 <when value="namesfile"> | 35 <when value="namesfile"> |
| 36 <param name="names" type="data" format="mothur.names" label="provide a names file" help="A names file will generate a new faste file containing all the sequences."/> | 36 <param name="names" type="data" format="mothur.names" label="provide a names file" help="A names file will generate a new faste file containing all the sequences."/> |
| 37 </when> | 37 </when> |
| 38 <when value="countfile"> | 38 <when value="countfile"> |
| 39 <param name="names" type="data" format="mothur.count_table" label="provide a count table" help="A counts table will generate a new faste file containing all the sequences. If the file contains group information, a group file will also be created."/> | 39 <param name="names" type="data" format="mothur.count_table" label="provide a count table" |
| 40 help="A counts table will generate a new faste file containing all the sequences. | |
| 41 If the file contains group information, a group file will also be created."/> | |
| 40 </when> | 42 </when> |
| 41 </conditional> | 43 </conditional> |
| 44 <expand macro="param-savelog"/> | |
| 42 </inputs> | 45 </inputs> |
| 43 <outputs> | 46 <outputs> |
| 44 <expand macro="logfile-output"/> | 47 <expand macro="logfile-output"/> |
| 45 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.redundant.fasta" label="${tool.name} on ${on_string}: fasta"/> | 48 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.redundant.fasta" label="${tool.name} on ${on_string}: fasta"/> |
| 46 <!-- groups file is created when a count file is used as input, but will be empty if the count file did not contain group information --> | 49 <!-- groups file is created when a count file is used as input, but will be empty if the count file did not contain group information --> |
| 52 <test><!-- test names file input --> | 55 <test><!-- test names file input --> |
| 53 <param name="fasta" value="amazon.unique.fasta"/> | 56 <param name="fasta" value="amazon.unique.fasta"/> |
| 54 <param name="intype" value="namesfile"/> | 57 <param name="intype" value="namesfile"/> |
| 55 <param name="names" value="amazon.unique.names"/> | 58 <param name="names" value="amazon.unique.names"/> |
| 56 <output name="out_fasta" md5="579698b8037ee939dd730e2cf0dd018d" ftype="fasta"/> | 59 <output name="out_fasta" md5="579698b8037ee939dd730e2cf0dd018d" ftype="fasta"/> |
| 60 <param name="savelog" value="true"/> | |
| 57 <expand macro="logfile-test"/> | 61 <expand macro="logfile-test"/> |
| 58 </test> | 62 </test> |
| 59 <test><!-- test count file input with group file output --> | 63 <test><!-- test count file input with group file output --> |
| 60 <param name="fasta" value="amazon.unique.fasta"/> | 64 <param name="fasta" value="amazon.unique.fasta"/> |
| 61 <param name="intype" value="countfile"/> | 65 <param name="intype" value="countfile"/> |
| 62 <param name="names" value="amazon_withgroups.count_table"/> | 66 <param name="names" value="amazon_withgroups.count_table"/> |
| 63 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/> | 67 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/> |
| 64 <output name="groups_file" file="amazon_withgroups.redundant.groups" ftype="mothur.groups"/> | 68 <output name="groups_file" file="amazon_withgroups.redundant.groups" ftype="mothur.groups"/> |
| 69 <param name="savelog" value="true"/> | |
| 65 <expand macro="logfile-test"/> | 70 <expand macro="logfile-test"/> |
| 66 </test> | 71 </test> |
| 67 <test><!-- test count file input without group file output --> | 72 <test><!-- test count file input without group file output --> |
| 68 <param name="fasta" value="amazon.unique.fasta"/> | 73 <param name="fasta" value="amazon.unique.fasta"/> |
| 69 <param name="intype" value="countfile"/> | 74 <param name="intype" value="countfile"/> |
| 70 <param name="names" value="amazon.count_table"/> | 75 <param name="names" value="amazon.count_table"/> |
| 71 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/> | 76 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/> |
| 72 <output name="groups_file" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.groups"/> <!--empty--> | 77 <output name="groups_file" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.groups"/> <!--empty--> |
| 78 <param name="savelog" value="true"/> | |
| 73 <expand macro="logfile-test"/> | 79 <expand macro="logfile-test"/> |
| 74 </test> | 80 </test> |
| 75 </tests> | 81 </tests> |
| 76 <help> | 82 <help><![CDATA[ |
| 77 <![CDATA[ | |
| 78 | 83 |
| 79 @MOTHUR_OVERVIEW@ | 84 @MOTHUR_OVERVIEW@ |
| 80 | 85 |
| 81 **Command Documentation** | 86 **Command Documentation** |
| 82 | 87 |
| 85 .. _name: https://www.mothur.org/wiki/Name_file | 90 .. _name: https://www.mothur.org/wiki/Name_file |
| 86 .. _deunique.seqs: https://www.mothur.org/wiki/Deunique.seqs | 91 .. _deunique.seqs: https://www.mothur.org/wiki/Deunique.seqs |
| 87 | 92 |
| 88 v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output | 93 v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output |
| 89 | 94 |
| 90 ]]> | 95 ]]></help> |
| 91 </help> | |
| 92 <expand macro="citations"/> | 96 <expand macro="citations"/> |
| 93 </tool> | 97 </tool> |