diff shuffling.xml @ 0:fae6527990af draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shuffling.xml	Thu May 21 03:58:09 2015 -0400
@@ -0,0 +1,59 @@
+<tool id="vsearch_shuffling" name="VSearch shuffling" 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@
+        --output $outfile
+        --seed $seed
+        --shuffle $infile
+        --topn $topn
+]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--shuffle)" />
+        <param name="seed" type="integer" value="0" label="Seed"
+            help="Zero to use random data source. (--seed)"/>
+        <expand macro="topn" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="db.fasta" ftype="fasta" />
+            <param name="seed" value="1"/>
+            <param name="topn" value="5"/>
+            <output name="outfile" file="shuffling_result1.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Sequence shuffling to obtain new random sequences.
+
+Shuffling options
+  --output FILENAME           output to specified FASTA file
+  --seed INT                  seed for PRNG, zero to use random data source (0)
+  --shuffle FILENAME          shuffle order of sequences pseudo-randomly
+  --topn INT                  output just first n sequences
+
+
+@EXTERNAL_DOCUMENTATION@
+
+-------
+
+@REFERENCES@
+
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>