diff dunovo.xml @ 6:9a0bee12b583 draft default tip

planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9fbe4b8871038d2945fa4b9ee0b5f89cf4e4f494\n'-dirty

--- a/dunovo.xml	Thu Dec 01 23:22:52 2016 -0500
+++ b/dunovo.xml	Mon Feb 06 23:39:11 2017 -0500
@@ -1,20 +1,20 @@
 <?xml version="1.0"?>
-<tool id="duplex" name="Du Novo: Make consensus reads" version="0.5">
+<tool id="duplex" name="Du Novo: Make consensus reads" version="0.6">
   <description>from duplex sequencing alignments</description>
   <requirements>
-    <requirement type="package" version="0.5">duplex</requirement>
+    <requirement type="package" version="0.6">duplex</requirement>
     <requirement type="set_environment">DUPLEX_DIR</requirement>
     <!-- TODO: require Python 2.7 -->
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
-    python \$DUPLEX_DIR/dunovo.py -r $min_reads -q $qual_thres -F $qual_format $input
+    python "\$DUPLEX_DIR/dunovo.py" -r $min_reads -q $qual_thres -F $qual_format '$input'
     #if $keep_sscs:
       --sscs-file sscs.fa
     #end if
     > duplex.fa
-    && python \$DUPLEX_DIR/utils/outconv.py duplex.fa -1 $dcs1 -2 $dcs2
+    && python "\$DUPLEX_DIR/utils/outconv.py" duplex.fa -1 '$dcs1' -2 '$dcs2'
     #if $keep_sscs:
-      && python \$DUPLEX_DIR/utils/outconv.py sscs.fa -1 $sscs1 -2 $sscs2
+      && python "\$DUPLEX_DIR/utils/outconv.py" sscs.fa -1 '$sscs1' -2 '$sscs2'
     #end if
   ]]>
   </command>
@@ -45,6 +45,22 @@
       <output name="dcs2" file="families.cons_2.fa"/>
     </test>
   </tests>
+  <citations>
+    <citation type="bibtex">@article{Stoler2016,
+      author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},
+      doi = {10.1186/s13059-016-1039-4},
+      issn = {1474-760X},
+      journal = {Genome biology},
+      number = {1},
+      pages = {180},
+      pmid = {27566673},
+      publisher = {Genome Biology},
+      title = {{Streamlined analysis of duplex sequencing data with Du Novo.}},
+      url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673},
+      volume = {17},
+      year = {2016}
+    }</citation>
+  </citations>
   <help>
 
 **What it does**