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

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

--- a/make_families.xml	Thu Dec 01 23:22:52 2016 -0500
+++ b/make_families.xml	Mon Feb 06 23:39:11 2017 -0500
@@ -1,16 +1,16 @@
 <?xml version="1.0"?>
-<tool id="make_families" name="Du Novo: Make families" version="0.5">
+<tool id="make_families" name="Du Novo: Make families" version="0.6">
   <description>of duplex sequencing reads</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>
   </requirements>
   <!-- TODO: Add dependency on coreutils to get paste? -->
-  <command>paste $fastq1 $fastq2
+  <command>paste '$fastq1' '$fastq2'
     | paste - - - -
-    | awk -f \$DUPLEX_DIR/make-barcodes.awk -v TAG_LEN=$taglen -v INVARIANT=$invariant
+    | awk -f "\$DUPLEX_DIR/make-barcodes.awk" -v TAG_LEN=$taglen -v INVARIANT=$invariant
     | sort
-    &gt; $output
+    &gt; '$output'
   </command>
   <inputs>
     <param name="fastq1" type="data" format="fastq" label="Sequencing reads, mate 1"/>
@@ -37,6 +37,22 @@
       <output name="output" file="smoke.families.i0.tsv"/>
     </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**