diff minimus2/minimus2.xml @ 0:937ba44abdb7 default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/minimus2/minimus2.xml	Tue Jun 07 17:29:43 2011 -0400
@@ -0,0 +1,55 @@
+<tool id="minimus2" name="Minimus2" version='1.0.1'>
+<description>Merge two sets of assembled contig sequences</description>
+<command interpreter='perl'>minimus2_wrapper.pl -tmpdir $contigs_outfile.extra_files_path $infile1 $infile2 $contigs_outfile $singletons_outfile
+#if $prefix1.select == 'y':
+-prefix1 $prefix1.prefix
+#end if
+#if $prefix2.select == 'y':
+-prefix2 $prefix2.prefix
+#end if
+</command>
+<inputs>
+    <param name="infile1" type="data" format="fasta" label="Contig sequences file 1"/>
+    <conditional name='prefix1'>
+        <param name='select' type='select' label='Rename contigs in file 1 by adding prefix?'>
+            <option value='y'>yes, add prefix</option>
+            <option value='n'>no, contig IDs are unique</option>
+        </param>
+        <when value='y'>
+            <param name="prefix" type="text" value="1" label="Prefix for sequences in file 1" />
+        </when>
+        <when value='n'>
+        </when>
+    </conditional>
+    <param name="infile2" type="data" format="fasta" label="Contig sequences file 2"/>
+    <conditional name='prefix2'>
+        <param name='select' type='select' label='Rename contigs in file 2 by adding prefix?'>
+            <option value='y'>yes, add prefix</option>
+            <option value='n'>no, contig IDs are unique</option>
+        </param>
+        <when value='y'>
+            <param name="prefix" type="text" value="2" label="Prefix for sequences in file 2" />
+        </when>
+        <when value='n'>
+        </when>
+    </conditional>
+</inputs>
+<outputs>
+    <data name="contigs_outfile" format="fasta" label="contigs" />
+    <data name="singletons_outfile" format="fasta" label="singletons" />
+</outputs>
+<help>
+**What it does**
+
+minimus2 is part of the AMOS assembler package, designed for merging one or two sets of contig sequences.
+
+This tool preprocesses the Fasta input files prior to coassembly with minimus2 and separately returns the new contigs
+and the sequences which did not co-assemble (singletons).
+
+The input sequences in each dataset must have unique IDs; use of the optional rename with prefix option avoids this.
+
+**Documentation**
+
+http://sourceforge.net/apps/mediawiki/amos/index.php?title=Minimus2
+</help>
+</tool>