Fix kraken2tax requirements and add test

.github/workflows/pr.yaml

@@ -164,16 +164,16 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04]
-        r-version: ['4.0.1']
+        r-version: ['release']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - uses: r-lib/actions/setup-r@master
+    - uses: r-lib/actions/setup-r@v2
       with:
         r-version: ${{ matrix.r-version }}
     - name: Cache R packages
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ${{ env.R_LIBS_USER }}
         key: r_cache_${{ matrix.os }}_${{ matrix.r-version }}
@@ -189,7 +189,7 @@ jobs:
     - name: lintr
       run: |
         library(lintr)
-        linters <- with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL)
+        linters <- linters_with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL)
         con <- file("repository_list.txt", "r")
         status <- 0
         while (TRUE) {
@@ -202,8 +202,8 @@ jobs:
             status <- 1
             for (l in lnt) {
               rel_path <- paste(repo, l$filename, sep="/")
-              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message), stderr())
-              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message), "rlint_report.txt", append=TRUE)
+              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message, paste("(", l$line, ")")), stderr())
+              write(paste(paste(rel_path, l$line_number, l$column_number, sep=":"), l$message, paste("(", l$line, ")")), "rlint_report.txt", append=TRUE)
             }
           }
         }

.tt_skip

@@ -4,7 +4,6 @@ tool_collections/hgv/hgv_hilbertvis
 tool_collections/hgv/snpfreq
 tool_collections/taxonomy/find_diag_hits
 tool_collections/taxonomy/gi2taxonomy
-tool_collections/taxonomy/kraken2tax
 tool_collections/taxonomy/lca_wrapper
 tool_collections/taxonomy/poisson2test
 tool_collections/taxonomy/t2ps

tool_collections/taxonomy/kraken2tax/kraken2tax.xml

@@ -1,8 +1,8 @@
-<tool id="Kraken2Tax" name="Convert Kraken" version="1.2">
+<tool id="Kraken2Tax" name="Convert Kraken" version="1.2+galaxy0">
   <description>data to Galaxy taxonomy representation</description>
     <requirements>
-        <requirement type="package" version="4.1.0">gawk</requirement>
-        <requirement type="package" version="1.0.0">gb_taxonomy_tools</requirement>
+        <requirement type="package" version="5.1.0">gawk</requirement>
+        <requirement type="package" version="1.0.1">gb_taxonomy_tools</requirement>
     </requirements>
   <command>
 <![CDATA[

tool_collections/taxonomy/kraken2tax/test-data/ncbi_taxonomy.loc.test

@@ -0,0 +1,2 @@
+#value	#name	path
+test	test	${__HERE__}/tax_dir

tool_collections/taxonomy/kraken2tax/test-data/tax_dir/names.dmp

@@ -0,0 +1,20 @@
+1	|	all	|		|	synonym	|
+1	|	root	|		|	scientific name	|
+2	|	Bacteria	|	Bacteria <prokaryote>	|	scientific name	|
+2	|	Monera	|	Monera <Bacteria>	|	in-part	|
+2	|	Procaryotae	|	Procaryotae <Bacteria>	|	in-part	|
+2	|	Prokaryota	|	Prokaryota <Bacteria>	|	in-part	|
+2	|	Prokaryotae	|	Prokaryotae <Bacteria>	|	in-part	|
+2	|	bacteria	|	bacteria <blast2>	|	blast name	|
+2	|	eubacteria	|		|	genbank common name	|
+2	|	not Bacteria Haeckel 1894	|		|	synonym	|
+2	|	prokaryote	|	prokaryote <Bacteria>	|	in-part	|
+2	|	prokaryotes	|	prokaryotes <Bacteria>	|	in-part	|
+6	|	Azorhizobium	|		|	scientific name	|
+6	|	Azorhizobium Dreyfus et al. 1988 emend. Lang et al. 2013	|		|	authority	|
+6	|	Azotirhizobium	|		|	misspelling	|
+7	|	ATCC 43989	|		|	type material	|
+7	|	Azorhizobium caulinodans	|		|	scientific name	|
+7	|	Azorhizobium caulinodans Dreyfus et al. 1988	|		|	synonym	|
+7	|	Azotirhizobium caulinodans	|		|	equivalent name	|
+7	|	CCUG 26647	|		|	type material	|

tool_collections/taxonomy/kraken2tax/test-data/tax_dir/nodes.dmp

@@ -0,0 +1,4 @@
+1	|	1	|	no rank	|		|	8	|	0	|	1	|	0	|	0	|	0	|	0	|	0	|		|
+2	|	2	|	superkingdom	|		|	0	|	0	|	11	|	0	|	0	|	0	|	0	|	0	|		|
+6	|	6	|	genus	|		|	0	|	1	|	11	|	1	|	0	|	1	|	0	|	0	|		|
+7	|	7	|	species	|	AC	|	0	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|

tool_collections/taxonomy/kraken2tax/tool_data_table_conf.xml.test

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of Kraken database in the required format -->
+    <table name="ncbi_taxonomy" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/ncbi_taxonomy.loc.test" />
+    </table>
+</tables>