diff augur_parse.xml @ 1:892c6690a1e8 draft default tip

planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty

--- a/augur_parse.xml	Fri Apr 05 13:45:27 2019 -0400
+++ b/augur_parse.xml	Mon Apr 08 13:27:08 2019 -0400
@@ -18,35 +18,30 @@
     <inputs>
         <param name="sequences" type="data" format="fasta" label="Sequences"/>
         <param name="fields" type="text" label="Fields in fasta header"/>
-	<param name="separator" type="text" value="|" label="Separator in fasta header"/>
+        <param name="separator" type="text" value="|" label="Separator in fasta header">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+                <mapping initial="none">
+                </mapping>
+            </sanitizer>
+        </param>
     </inputs>
     <outputs>
-      <data name="output_sequences" format="fasta" />
-      <data name="output_metadata" format="tabular" />
+        <data name="output_sequences" format="fasta" />
+        <data name="output_metadata" format="tabular" />
     </outputs>
     <tests>
         <test>
-          <param name="sequences" value="test_00_sequences.input.fasta" />
-	  <param name="fields" value="strain country year" />
-	  <output name="output_sequences" file="test_00_sequences.output.fasta" />
-	  <output name="output_metadata" file="test_00_metadata.output.fasta" />
+            <param name="sequences" value="augur_parse_test_0_sequences.input.fasta" />
+            <param name="fields" value="strain country year" />
+            <output name="output_sequences" file="augur_parse_test_0_sequences.output.fasta" />
+            <output name="output_metadata" file="augur_parse_test_0_metadata.output.csv" />
         </test>
     </tests>
     <help><![CDATA[
 Parse delimited fields from FASTA sequence names into a TSV and FASTA file.
     ]]></help>
-    <citations>
-        <citation type="bibtex">
-	  @article{hadfield2018nextstrain,
-	    title={Nextstrain: real-time tracking of pathogen evolution},
-	    author={Hadfield, James and Megill, Colin and Bell, Sidney M and Huddleston, John and Potter, Barney and Callender, Charlton and Sagulenko, Pavel and Bedford, Trevor and Neher, Richard A},
-	    journal={Bioinformatics},
-	    volume={34},
-	    number={23},
-	    pages={4121--4123},
-	    year={2018},
-	    publisher={Oxford University Press}
-	  }
-	</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>