Mercurial > repos > iuc > mothur_unique_seqs
comparison unique.seqs.xml @ 2:837f454548b8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 21:58:25 -0400 |
| parents | 0468cb2dd83e |
| children | a033f325ad8d |
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| 1:1f72d9a3d09f | 2:837f454548b8 |
|---|---|
| 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 "$names" names.dat && | 13 ln -s '$names' names.dat && |
| 14 ln -s "$fasta" fasta.dat && | 14 ln -s '$fasta' fasta.dat && |
| 15 | 15 |
| 16 echo 'unique.seqs( | 16 echo 'unique.seqs( |
| 17 #if $names.is_of_type('mothur.names'): | 17 #if $names.is_of_type('mothur.names'): |
| 18 name=names.dat, | 18 name=names.dat, |
| 19 #elif $names.is_of_type('mothur.count_table'): | 19 #elif $names.is_of_type('mothur.count_table'): |
| 20 count=names.dat, | 20 count=names.dat, |
| 21 #end if | 21 #end if |
| 22 fasta=fasta.dat | 22 fasta=fasta.dat, |
| 23 )' | 23 format=$format |
| 24 | sed 's/ //g' ## mothur trips over whitespace | 24 )' |
| 25 | mothur | 25 | sed 's/ //g' ## mothur trips over whitespace |
| 26 | tee mothur.out.log | 26 | mothur |
| 27 | tee mothur.out.log | |
| 27 ]]></command> | 28 ]]></command> |
| 28 <inputs> | 29 <inputs> |
| 29 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> | 30 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> |
| 30 <param name="names" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Names"/> | 31 <param name="names" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Names"/> |
| 32 <param name="format" type="select" label="output format"> | |
| 33 <option value="count" selected="true"> Count table </option> | |
| 34 <option value="name"> Name file </option> | |
| 35 </param> | |
| 36 <expand macro="param-savelog"/> | |
| 31 </inputs> | 37 </inputs> |
| 32 <outputs> | 38 <outputs> |
| 33 <expand macro="logfile-output"/> | 39 <expand macro="logfile-output"/> |
| 34 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/> | 40 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/> |
| 35 <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names"> | 41 <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names"> |
| 36 <filter>names.ext != "mothur.count_table"</filter> | 42 <filter> format == "name" </filter> |
| 37 </data> | 43 </data> |
| 38 <data name="out_count" format="mothur.count_table" from_work_dir="fasta*.count_table" label="${tool.name} on ${on_string}: count_table"> | 44 <data name="out_count" format="mothur.count_table" from_work_dir="fasta*.count_table" label="${tool.name} on ${on_string}: count_table"> |
| 39 <filter>names and names.ext == "mothur.count_table"</filter> | 45 <filter> format == "count" </filter> |
| 40 </data> | 46 </data> |
| 41 </outputs> | 47 </outputs> |
| 42 <tests> | 48 <tests> |
| 43 <test><!-- test with names file --> | 49 <test><!-- test with names file --> |
| 44 <param name="fasta" value="amazon.fasta"/> | 50 <param name="fasta" value="amazon.fasta"/> |
| 45 <param name="names" value="amazon1.names" ftype="mothur.names"/> | 51 <param name="names" value="amazon1.names" ftype="mothur.names"/> |
| 52 <param name="format" value="name"/> | |
| 46 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/> | 53 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/> |
| 47 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/> | 54 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/> |
| 55 <param name="savelog" value="true"/> | |
| 48 <expand macro="logfile-test"/> | 56 <expand macro="logfile-test"/> |
| 49 </test> | 57 </test> |
| 50 <test><!-- test with count file --> | 58 <test><!-- test with count file --> |
| 51 <param name="fasta" value="amazon.unique.fasta"/> | 59 <param name="fasta" value="amazon.unique.fasta"/> |
| 52 <param name="names" value="amazon.count_table" ftype="mothur.count_table"/> | 60 <param name="names" value="amazon.count_table" ftype="mothur.count_table"/> |
| 53 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/> | 61 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/> |
| 54 <output name="out_count" md5="2024cbb895f79346606ab196dd130639" ftype="mothur.count_table"/> | 62 <output name="out_count" md5="2024cbb895f79346606ab196dd130639" ftype="mothur.count_table"/> |
| 63 <param name="savelog" value="true"/> | |
| 55 <expand macro="logfile-test"/> | 64 <expand macro="logfile-test"/> |
| 56 </test> | 65 </test> |
| 57 <test><!-- test wth fasta only --> | 66 <test><!-- test wth fasta only --> |
| 58 <param name="fasta" value="amazon.fasta"/> | 67 <param name="fasta" value="amazon.fasta"/> |
| 68 <param name="format" value="name"/> | |
| 59 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/> | 69 <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/> |
| 60 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/> | 70 <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/> |
| 71 <param name="savelog" value="true"/> | |
| 61 <expand macro="logfile-test"/> | 72 <expand macro="logfile-test"/> |
| 62 </test> | 73 </test> |
| 63 </tests> | 74 </tests> |
| 64 <help> | 75 <help><![CDATA[ |
| 65 <![CDATA[ | |
| 66 | 76 |
| 67 @MOTHUR_OVERVIEW@ | 77 @MOTHUR_OVERVIEW@ |
| 68 | 78 |
| 69 **Command Documentation** | 79 **Command Documentation** |
| 70 | 80 |
| 71 The unique.seqs_ command returns only the unique sequences found in a fasta-formatted sequence file and a name_ file that indicates those sequences that are identical to the reference sequence. | 81 The unique.seqs_ command returns only the unique sequences found in a fasta-formatted sequence file and a name_ file that indicates those sequences that are identical to the reference sequence. |
| 72 | 82 |
| 73 .. _name: https://www.mothur.org/wiki/Name_file | 83 .. _name: https://www.mothur.org/wiki/Name_file |
| 74 .. _unique.seqs: https://www.mothur.org/wiki/Unique.seqs | 84 .. _unique.seqs: https://www.mothur.org/wiki/Unique.seqs |
| 75 | 85 |
| 76 ]]> | 86 ]]></help> |
| 77 </help> | |
| 78 <expand macro="citations"/> | 87 <expand macro="citations"/> |
| 79 </tool> | 88 </tool> |