Linter fixes for vcflib (galaxyproject#6391)

* fix redundant argumen/name

* use vcflib citation for vcfsort

even if its just command line

tool_collections/vcflib/vcffilter/vcffilter.xml

@@ -49,11 +49,11 @@ input1.vcf.gz
                 <validator type="expression" message="Invalid operator provided, valid operators are =, !, &lt;, &gt;, |, &amp;.">value is not None and not any(x in value for x in ["&lt;=", "=&lt;", "&gt;=", "=&gt;"])</validator>
             </param>
         </repeat>
-        <param name="filter_sites" argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/>
-        <param name="tag_pass" argument="--tag-pass" type="boolean" truevalue="--tag-pass" falsevalue="" label="Tag vcf records as positively filtered with this tag, print all records"/>
-        <param name="tag_fail" argument="--tag-fail" type="boolean" truevalue="--tag-fail" falsevalue="" label="Tag vcf records as negatively filtered with this tag, print all records"/>
-        <param name="append_filter" argument="--append-filter" type="boolean" truevalue="--append-filter" falsevalue="" label="Append the existing filter tag, don't just replace it"/>
-        <param name="allele_tag" argument="--allele-tag" type="boolean" truevalue="--allele-tag" falsevalue="" label="Apply --tag-pass on a per-allele basis, adds or sets the corresponding INFO field tag"/>
+        <param argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/>
+        <param argument="--tag-pass" type="boolean" truevalue="--tag-pass" falsevalue="" label="Tag vcf records as positively filtered with this tag, print all records"/>
+        <param argument="--tag-fail" type="boolean" truevalue="--tag-fail" falsevalue="" label="Tag vcf records as negatively filtered with this tag, print all records"/>
+        <param argument="--append-filter" type="boolean" truevalue="--append-filter" falsevalue="" label="Append the existing filter tag, don't just replace it"/>
+        <param argument="--allele-tag" type="boolean" truevalue="--allele-tag" falsevalue="" label="Apply --tag-pass on a per-allele basis, adds or sets the corresponding INFO field tag"/>
         <param argument="--invert" type="boolean" truevalue="--invert" falsevalue="" label="Inverts the filter, e.g. grep -v"/>
         <param argument="--or" type="boolean" truevalue="--or" falsevalue="" label="Use logical OR instead of AND to combine filters"/>
         <param argument="--region" type="text" label="Specify a region on which to target the filtering" help="Regions should be specified as chr:start-end, e.g X:1000-2000"/>

tool_collections/vcflib/vcfsort/vcfsort.xml

@@ -30,4 +30,5 @@ This tool uses native UNIX sort command to order VCF dataset in coordinate order
 
 The same result can be achieved with the Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order).
     </help>
+    <expand macro="citations" />
 </tool>