# HG changeset patch
# User iuc
# Date 1742938023 0
# Node ID 2559b7ce2114c49a538d557d62bf280bb3b0c7c5
# Parent  32d058f3462a660ac1e69fa17e0584ea1a4da36d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx commit 14178ea62ed017f16cb0d4ff85fdfdc61dd3b69e

diff -r 32d058f3462a -r 2559b7ce2114 macros.xml
--- a/macros.xml	Thu Nov 21 02:20:02 2024 +0000
+++ b/macros.xml	Tue Mar 25 21:27:03 2025 +0000
@@ -5,8 +5,8 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">0.5.4</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">0.5.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="biotools">
         <xrefs>
diff -r 32d058f3462a -r 2559b7ce2114 ncbi_fcs_gx.xml
--- a/ncbi_fcs_gx.xml	Thu Nov 21 02:20:02 2024 +0000
+++ b/ncbi_fcs_gx.xml	Tue Mar 25 21:27:03 2025 +0000
@@ -34,9 +34,12 @@
         --species '$mode.species'
     #end if
         --split-fasta '$mode.screen_adv.split_fasta'
-    #if $mode.screen_adv.div:
+    #if $mode.screen_adv.div
         --div '$mode.screen_adv.div'
     #end if
+    #if $mode.screen_adv.ignore_same_kingdom
+        --ignore-same-kingdom
+    #end if
         --gx-db "\${TMPDIR}"
         --out-basename output
         --action-report true
@@ -111,6 +114,7 @@
                     </param>
                     <param argument="--split-fasta" type="boolean" checked="true" optional="true" label="Split fasta sequences on N-runs of length at least 10"/>
                     <param argument="--div" type="text" value="" optional="true" label="BLAST-div of the tax-id" help="from 'NCBI BLAST name' on taxon Info page"/>
+                    <param argument="--ignore-same-kingdom" type="boolean" checked="false" optional="true" label="Ignore same-kingdom contamination"/>
                 </section>
             </when>
             <when value="clean">
diff -r 32d058f3462a -r 2559b7ce2114 test-data/output.fcs_gx_report.txt
--- a/test-data/output.fcs_gx_report.txt	Thu Nov 21 02:20:02 2024 +0000
+++ b/test-data/output.fcs_gx_report.txt	Tue Mar 25 21:27:03 2025 +0000
@@ -1,7 +1,7 @@
-##[["FCS genome report", 2, 1], {"git-rev": "v0.5.4-5-g5dfd516", "run-date": "Thu Sep  5 19:38:38 2024", "db": {"build-date": "2022-11-03", "seqs": 3042, "Gbp": 0.28336}, "run-info": {"agg-cvg": 0.455294, "asserted-div": "anml:insects", "inferred-primary-divs": ["prok:CFB group bacteria"], "corrected-primary-divs": ["anml:insects"], "genome-hash": "dbb3380351f70e9b"}}]
+##[["FCS genome report", 2, 1], {"git-rev": "v0.5.5-9-gfc836c1", "run-date": "Tue Mar 25 16:04:25 2025", "db": {"build-date": "2022-11-03", "seqs": 3042, "Gbp": 0.28336}, "run-info": {"agg-cvg": 0.454486, "asserted-div": "anml:insects", "inferred-primary-divs": ["prok:CFB group bacteria"], "corrected-primary-divs": ["anml:insects"], "genome-hash": "dbb3380351f70e9b"}}]
 #seq_id	start_pos	end_pos	seq_len	action	div	agg_cont_cov	top_tax_name
 JPZV02005859.1	1	705930	705930	REVIEW	prok:CFB group bacteria	31	Bacteroides salyersiae
-JPZV02009577.1	1	600722	600722	EXCLUDE	prok:CFB group bacteria	61	Bacteroides bouchesdurhonensis
+JPZV02009577.1	1	600722	600722	EXCLUDE	prok:CFB group bacteria	61	Bacteroides caecimuris
 JPZV02016362.1	1	432265	432265	EXCLUDE	prok:CFB group bacteria	54	Bacteroides caecimuris
 JPZV02031416.1	1	170387	170387	REVIEW	prok:CFB group bacteria	28	Bacteroides caecimuris
 JPZV02034235.1	1	131158	131158	EXCLUDE	prok:CFB group bacteria	38	Bacteroides massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223
diff -r 32d058f3462a -r 2559b7ce2114 test-data/output.taxonomy.rpt
--- a/test-data/output.taxonomy.rpt	Thu Nov 21 02:20:02 2024 +0000
+++ b/test-data/output.taxonomy.rpt	Tue Mar 25 21:27:03 2025 +0000
@@ -1,7 +1,7 @@
-##[["GX taxonomy analysis report", 3, 1], {"git-rev": "v0.5.4-5-g5dfd516", "run-date": "Thu Sep  5 19:38:38 2024", "db": {"build-date": "2022-11-03", "seqs": 3042, "Gbp": 0.28336}, "run-info": {"agg-cvg": 0.455294, "asserted-div": "anml:insects", "inferred-primary-divs": ["prok:CFB group bacteria"], "corrected-primary-divs": ["anml:insects"], "genome-hash": "dbb3380351f70e9b"}}]
+##[["GX taxonomy analysis report", 3, 1], {"git-rev": "v0.5.5-9-gfc836c1", "run-date": "Tue Mar 25 16:04:25 2025", "db": {"build-date": "2022-11-03", "seqs": 3042, "Gbp": 0.28336}, "run-info": {"agg-cvg": 0.454486, "asserted-div": "anml:insects", "inferred-primary-divs": ["prok:CFB group bacteria"], "corrected-primary-divs": ["anml:insects"], "genome-hash": "dbb3380351f70e9b"}}]
 #seq-id	seq-len	(xp,lc,co,n,mt,pt,pm)-len	cvg-by-all	sep1	tax-name-1	tax-id-1	div-1	cvg-by-div-1	cvg-by-tax-1	score-1	sep2	tax-id-2	div-2	cvg-by-div-2	cvg-by-tax-2	score-2	sep3	tax-id-3	div-3	cvg-by-div-3	cvg-by-tax-3	score-3	sep4	tax-id-4	div-4	cvg-by-div-4	cvg-by-tax-4	score-4	sep5	reserved	result	div	div_pct_cvg
 JPZV02005859.1	705930	0,1139,0,0,0,0,0	227139	|	Bacteroides salyersiae	291644	prok:CFB group bacteria	227139	47267	364	|	1796613	prok:CFB group bacteria	227139	40278	342	|						|						|	n/a	low-coverage	prok:CFB group bacteria	32
-JPZV02009577.1	600722	0,65,0,0,0,0,0	374876	|	Bacteroides bouchesdurhonensis	1841855	prok:CFB group bacteria	374876	122690	746	|	1796613	prok:CFB group bacteria	374876	125102	742	|						|						|	n/a	contaminant(div)	prok:CFB group bacteria	62
+JPZV02009577.1	600722	0,65,0,0,0,0,0	373207	|	Bacteroides caecimuris	1796613	prok:CFB group bacteria	373207	125070	743	|	329854	prok:CFB group bacteria	373207	120705	728	|						|						|	n/a	contaminant(div)	prok:CFB group bacteria	62
 JPZV02016362.1	432265	0,0,0,0,0,0,0	238387	|	Bacteroides caecimuris	1796613	prok:CFB group bacteria	238387	78677	508	|	1852362	prok:CFB group bacteria	238387	76183	487	|						|						|	n/a	contaminant(div)	prok:CFB group bacteria	55
 JPZV02031416.1	170387	0,60,0,0,0,0,0	48647	|	Bacteroides caecimuris	1796613	prok:CFB group bacteria	48647	16469	208	|	435590	prok:CFB group bacteria	48647	15004	201	|						|						|	n/a	low-coverage	prok:CFB group bacteria	29
 JPZV02034235.1	131158	0,0,0,0,0,0,0	50739	|	Bacteroides massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223	1121098	prok:CFB group bacteria	50739	27281	262	|	871325	prok:CFB group bacteria	50739	19889	228	|						|						|	n/a	contaminant(div)	prok:CFB group bacteria	39