diff tools/maf/maf_reverse_complement.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/maf/maf_reverse_complement.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,53 @@
+<tool id="MAF_Reverse_Complement_1" name="Reverse Complement" version="1.0.1">
+  <description>a MAF file</description>
+  <command interpreter="python">maf_reverse_complement.py $input1 $out_file1 $species</command>
+  <inputs>
+    <page>
+        <param format="maf" name="input1" label="Alignment File" type="data"/>
+        <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
+          <options>
+            <filter type="data_meta" ref="input1" key="species" />
+          </options>
+        </param>
+    </page>
+   </inputs>
+  <outputs>
+    <data format="maf" name="out_file1" metadata_source="input1"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="3.maf" dbkey="hg17" format="maf"/>
+      <param name="species" value="hg17,panTro1,mm5,rn3,canFam1"/>
+      <output name="out_file1" file="maf_reverse_complement_out.dat"/>
+    </test>
+  </tests>
+  <help>
+**What it does**
+
+This tool takes a MAF file and creates a new MAF file, where each block has been reversed complemented.
+
+**Example**
+  
+This MAF Block::
+
+  a score=8157.000000
+  s hg17.chr7    127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
+  s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
+  s mm5.chr6      28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG
+
+becomes::
+
+  a score=8157.000000
+  s hg17.chr7     31156555 58 - 158628139 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAATGAATAAACCACAAATT
+  s panTro1.chr6  31691510 58 - 161576975 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAACGAATAAACCACAAATT
+  s mm5.chr6     120816549 54 - 149721531 CCTCTTCCACTGAGGAATTTCTTTTTTTAAATGATGAGCAATCAATGAAACG----TT
+
+------
+
+**Citation**
+
+If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21775304&gt;`_
+
+
+  </help>
+</tool>