diff obiuniq.xml @ 0:4c2b715a258a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2

--- /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>