From f28d66c0bcad8ac29be2afec28bc639317239775 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 1 Oct 2024 15:39:32 +0200
Subject: [PATCH] Linter fixes for vcflib (#6391)

* fix redundant argumen/name

* use vcflib citation for vcfsort

even if its just command line
---
 tool_collections/vcflib/vcffilter/.lint_skip    |  1 -
 tool_collections/vcflib/vcffilter/vcffilter.xml | 10 +++++-----
 tool_collections/vcflib/vcfsort/.lint_skip      |  1 -
 tool_collections/vcflib/vcfsort/vcfsort.xml     |  1 +
 4 files changed, 6 insertions(+), 7 deletions(-)
 delete mode 100644 tool_collections/vcflib/vcffilter/.lint_skip
 delete mode 100644 tool_collections/vcflib/vcfsort/.lint_skip

diff --git a/tool_collections/vcflib/vcffilter/.lint_skip b/tool_collections/vcflib/vcffilter/.lint_skip
deleted file mode 100644
index e7d00398ee9..00000000000
--- a/tool_collections/vcflib/vcffilter/.lint_skip
+++ /dev/null
@@ -1 +0,0 @@
-InputsNameRedundantArgument
diff --git a/tool_collections/vcflib/vcffilter/vcffilter.xml b/tool_collections/vcflib/vcffilter/vcffilter.xml
index 5b0c06ef1c9..6d7f3a643d4 100644
--- a/tool_collections/vcflib/vcffilter/vcffilter.xml
+++ b/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"/>
diff --git a/tool_collections/vcflib/vcfsort/.lint_skip b/tool_collections/vcflib/vcfsort/.lint_skip
deleted file mode 100644
index 46f5e08e85b..00000000000
--- a/tool_collections/vcflib/vcfsort/.lint_skip
+++ /dev/null
@@ -1 +0,0 @@
-CitationsMissing
diff --git a/tool_collections/vcflib/vcfsort/vcfsort.xml b/tool_collections/vcflib/vcfsort/vcfsort.xml
index 2a62f61a6a1..4731838146e 100644
--- a/tool_collections/vcflib/vcfsort/vcfsort.xml
+++ b/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>