diff dereplication.xml @ 0:fae6527990af draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dereplication.xml	Thu May 21 03:58:09 2015 -0400
@@ -0,0 +1,93 @@
+<tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.0">
+    <description></description>
+    <macros>
+        <import>vsearch_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+    vsearch
+        @GENERAL@
+        --derep_fulllength $infile
+        #if $maxuniquesize:
+            --maxuniquesize $maxuniquesize
+        #end if
+        #if $minuniquesize:
+            --minuniquesize $minuniquesize
+        #end if
+        --output $outfile
+        #if $sizein:
+            --sizein $sizein
+        #end if
+        #if $sizeout:
+            --sizeout $sizeout
+        #end if
+        --strand $strand
+        --topn $topn
+        #if $uc:
+            --uc $uc
+        #end if
+]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--derep_fulllength)" />
+        <expand macro="topn" />
+        <expand macro="sizein" />
+        <expand macro="sizeout" />
+        <expand macro="strand" />
+        <expand macro="uclust_like_output" />
+        <param name="minuniquesize" type="integer" value="" optional="True" label="Minimum abundance"
+            help="(--minuniquesize)"/>
+        <param name="maxuniquesize" type="integer" value="" optional="True" label="Maximum abundance"
+            help="(--maxuniquesize)"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
+        <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output">
+            <filter>uc is True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
+            <param name="strand" value="both" />
+            <param name="minuniquesize" value="1" />
+            <param name="maxuniquesize" value="100000" />
+            <param name="sizeout" value="--sizeout"/>
+            <param name="topn" value="10000" />
+            <output name="outfile" file="dereplication_result1.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Merge strictly identical sequences contained in filename. Identical sequences are
+defined as having the same length and the same string of nucleotides (case insensitive,
+T and U are considered the same).
+
+Dereplication options
+  --derep_fulllength FILENAME  dereplicate sequences in the given FASTA file
+  --maxuniquesize INT          maximum abundance for output from dereplication
+  --minuniquesize INT          minimum abundance for output from dereplication
+  --output FILENAME            output FASTA file
+  --sizein                     read abundance annotation from input
+  --sizeout                    write abundance annotation to output
+  --strand                     dereplicate "plus" or "both" strands (plus)
+  --topn INT                   output just the n most abundant sequences
+  --uc FILENAME                filename for UCLUST-like output
+
+
+@EXTERNAL_DOCUMENTATION@
+
+-------
+
+@REFERENCES@
+
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>