Mercurial > repos > iuc > obi_uniq
diff obiuniq.xml @ 0:4c2b715a258a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
author | iuc |
---|---|
date | Wed, 12 Apr 2017 17:38:18 -0400 |
parents | |
children | e0655b546470 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/obiuniq.xml Wed Apr 12 17:38:18 2017 -0400 @@ -0,0 +1,92 @@ +<tool id="obi_uniq" name="obiuniq" version="@WRAPPER_VERSION@"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> +<command> + + <![CDATA[ + + obiuniq + #if str( $options_attribute) == "merge" + -m '$options_uniq' + #else + -c '$options_uniq' + #end if + ${mid} + ${prefix} + '$input' > '$output' + + ]]> + +</command> + +<inputs> + <param name="input" type="data" format="fasta,fastq" label="Input sequences file" /> + <param name="options_uniq" type="select" label="Attribute to merge" > + <expand macro="attributes"/> + </param> + <param name="options_attribute" type="select" label="Use specific option" > + <option value="merge" selected="true">merge</option> + <option value="category_attribute">category_attribute</option> + </param> + <param name="mid" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Add a merged attribute containing the list of sequence record ids merged within this group" /> + <param name="prefix" type="boolean" checked="false" truevalue="-p" falsevalue="" label="Dereplicate through a prefix matching" /> +</inputs> +<outputs> + <data format="fasta" name="output" label="output.fasta with ${tool.name} on ${on_string}" /> +</outputs> + +<tests> + <test> + <param name="input" value="output_ngsfilter_error_3.fastq" /> + <param name="options_uniq" value="sample" /> + <param name="options_attribute" value="merge" /> + <param name="mid" value="False" /> + <param name="prefix" value="False" /> + <output name="output" file="output_obiuniq.fasta" ftype="fasta"/> + </test> + <test> + <param name="input" value="output_ngsfilter_error_3.fastq" /> + <param name="options_uniq" value="family" /> + <param name="options_attribute" value="category_attribute" /> + <param name="mid" value="True" /> + <param name="prefix" value="True" /> + <output name="output" file="output_obiuniq_family.fasta" ftype="fasta"/> + </test> + +</tests> +<help><![CDATA[ + +.. class:: infomark + +**What it does** + +The obiuniq command is in some way analog to the standard Unix uniq -c command. + +Instead of working text line by text line as the standard Unix tool, the processing is done on sequence records. + +A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself. + +The obiuniq command groups together sequence records. Then, for each group, a sequence record is printed. + +A group is defined by the sequence and optionally by the values of a set of attributes specified with the -c option. + +As the identifier, the set of attributes (key=value) and the definition of the sequence records that are grouped together may be different, two options (-m and -i) allow refining how these parts of the records are reported. + +\* By default, only attributes with identical values within a group of sequence records are kept. + +\* A count attribute is set to the total number of sequence records for each group. + +\* For each attribute specified by the -m option, a new attribute whose key is prefixed by merged_ is created. These new attributes contain the number of times each value occurs within the group of sequence records. + + +@OBITOOLS_LINK@ + + + +]]> +</help> +<expand macro="citation" /> +</tool>