Mercurial > repos > iuc > mothur_unique_seqs
diff unique.seqs.xml @ 0:4098a8c01660 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
| author | iuc |
|---|---|
| date | Fri, 24 Jun 2016 16:54:29 -0400 |
| parents | |
| children | a8d6c0935377 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/unique.seqs.xml Fri Jun 24 16:54:29 2016 -0400 @@ -0,0 +1,55 @@ +<tool profile="16.07" id="mothur_unique_seqs" name="Unique.seqs" version="@WRAPPER_VERSION@.0"> + <description>Return unique sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="aggressive"><![CDATA[ + ## create symlinks to input datasets + ln -s "$names" names.dat && + ln -s "$fasta" fasta.dat && + + echo 'unique.seqs( + #if $names: + name=names.dat, + #end if + fasta=fasta.dat + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + ]]></command> + <inputs> + <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> + <param name="names" type="data" format="mothur.names" optional="true" label="names - Sequences Names"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.unique.*" label="${tool.name} on ${on_string}: fasta"/> + <data name="out_names" format="mothur.names" from_work_dir="fasta*.names" label="${tool.name} on ${on_string}: names"/> + </outputs> + <tests> + <test> + <param name="fasta" value="amazon.fasta"/> + <param name="names" value="amazon.names"/> + <output name="out_fasta" file="amazon.unique.fasta" ftype="fasta"/> + <output name="out_names" file="amazon.unique.names" ftype="mothur.names"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documenation** + +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. + +.. _name: http://www.mothur.org/wiki/Name_file +.. _unique.seqs: http://www.mothur.org/wiki/Unique.seqs + +]]> + </help> + <expand macro="citations"/> +</tool>