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changeset 11:7f1cfa4c0e32 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a14db40361bcb2ee608bccd9222e1654aaea3324
author iuc
date Wed, 11 Jan 2023 09:56:04 +0000
parents ee29337f905c
children 8c05afb547fa
files ivar_removereads.xml macros.xml test-data/zika/Z52.consensus.fa.fai test-data/zika/Z52.consensus.qual.txt test-data/zika/Z52_a.sorted.bam.bai test-data/zika/Z52_a.trimmed.sorted.bam.bai test-data/zika/Z52_a.tsv test-data/zika/Z52_a.vcf test-data/zika/Z52_a_annotated.tsv test-data/zika/Z52_a_pass.vcf test-data/zika/Z52_b.sorted.bam.bai test-data/zika/Z52_b.trimmed.sorted.bam.bai test-data/zika/db/PRV.gff test-data/zika/primer_mismatchers_indices.txt
diffstat 14 files changed, 74 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/ivar_removereads.xml	Wed Jul 13 15:20:33 2022 +0000
+++ b/ivar_removereads.xml	Wed Jan 11 09:56:04 2023 +0000
@@ -1,12 +1,10 @@
-<tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy3" profile="21.01">
+<tool id="ivar_removereads" name="ivar removereads" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
     <description>Remove reads from trimmed BAM file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="3.8.1">python</requirement>
-    </expand>
-    <expand macro="version_command" />
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
         cp '$input_bed' binding_sites.bed &&
         python '$__tool_directory__/sanitize_bed.py' binding_sites.bed &&
@@ -31,10 +29,10 @@
     <inputs>
         <param name="input_bam" argument="-i" type="data" format="bam"
         label="Bam input"
-        help="BAM dataset, preprocessed with ivar trim, to remove reads from" />
+        help="BAM dataset, preprocessed with ivar trim, to remove reads from"/>
         <param name="variants_tsv" type="data" format="tabular"
         label="Variants input"
-        help="This dataset will be scanned for variants that affect primer binding sites and needs to be in tabular format with affected chromosome names in the first, and positions in the second column. If there is a header line, the name of the second column should be POS." />
+        help="This dataset will be scanned for variants that affect primer binding sites and needs to be in tabular format with affected chromosome names in the first, and positions in the second column. If there is a header line, the name of the second column should be POS."/>
         <param name="input_bed" argument="-b" type="data" format="bed" label="Primer binding sites information"
         help="The same six-column BED dataset that served as input to ivar trim"/>
         <conditional name="amplicons">
@@ -59,19 +57,27 @@
             <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
             <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
             <conditional name="amplicons">
-                <param name="computed" value="no" />
+                <param name="computed" value="no"/>
                 <param name="amplicon_info" value="zika/db/pair_information.tsv"/>
             </conditional>
-            <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
+            <output name="output_bam" ftype="bam">
+                <assert_contents>
+                    <has_size value="3185672" delta="1000"/>
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
             <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
             <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
             <conditional name="amplicons">
-                <param name="computed" value="yes" />
+                <param name="computed" value="yes"/>
             </conditional>
-            <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
+            <output name="output_bam" ftype="bam">
+                <assert_contents>
+                    <has_size value="3185672" delta="1000"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
--- a/macros.xml	Wed Jul 13 15:20:33 2022 +0000
+++ b/macros.xml	Wed Jan 11 09:56:04 2023 +0000
@@ -1,10 +1,14 @@
+<?xml version="1.0"?>
 <macros>
-  <token name="@VERSION@">1.3.1</token>
+  <token name="@TOOL_VERSION@">1.3.1</token>
+  <token name="@PROFILE@">21.01</token>
   <xml name="requirements">
-    <requirements>
-      <requirement type="package" version="@VERSION@">ivar</requirement>
-      <yield />
-    </requirements>
+  <requirements>
+      <requirement type="package" version="@TOOL_VERSION@">ivar</requirement>
+      <requirement type="package" version="3.10.8">python</requirement>
+      <requirement type="package" version="1.16">samtools</requirement>
+      <yield/>
+  </requirements>
   </xml>
   <xml name="version_command">
     <version_command>ivar version | grep version</version_command>
@@ -12,7 +16,7 @@
   <xml name="citations">
     <citations>
       <citation type="doi">10.1186/s13059-018-1618-7</citation>
-      <yield />
+      <yield/>
     </citations>
   </xml>
 </macros>
--- a/test-data/zika/Z52.consensus.fa.fai	Wed Jul 13 15:20:33 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-Consensus_Z52.consensus_threshold_0_quality_20	10139	48	10139	10140
--- a/test-data/zika/Z52.consensus.qual.txt	Wed Jul 13 15:20:33 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
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Binary file test-data/zika/Z52_a.sorted.bam.bai has changed
Binary file test-data/zika/Z52_a.trimmed.sorted.bam.bai has changed
--- a/test-data/zika/Z52_a.tsv	Wed Jul 13 15:20:33 2022 +0000
+++ b/test-data/zika/Z52_a.tsv	Wed Jan 11 09:56:04 2023 +0000
@@ -9,7 +9,7 @@
 PRV	3148	Y	T	0	0	0	1324	264	36	0.77563	1707	0	TRUE	NA	NA	NA	NA	NA
 PRV	3148	Y	C	0	0	0	381	75	36	0.223199	1707	0	TRUE	NA	NA	NA	NA	NA
 PRV	3295	A	G	1002	1002	35	38	38	33	0.0365385	1040	4.30837e-11	TRUE	NA	NA	NA	NA	NA
-PRV	5680	C	T	27	5	44	8	2	46	0.228571	35	0.000596701	TRUE	NA	NA	NA	NA	NA
+PRV	5680	C	T	27	10	44	8	3	46	0.228571	35	0.000596701	TRUE	NA	NA	NA	NA	NA
 PRV	5723	T	G	31	31	35	1	1	21	0.03125	32	0.507937	FALSE	NA	NA	NA	NA	NA
 PRV	6201	A	G	10	0	35	2	0	38	0.166667	12	0.26087	FALSE	NA	NA	NA	NA	NA
 PRV	6211	T	C	8	0	36	1	0	35	0.111111	9	0.5	FALSE	NA	NA	NA	NA	NA
--- a/test-data/zika/Z52_a.vcf	Wed Jul 13 15:20:33 2022 +0000
+++ b/test-data/zika/Z52_a.vcf	Wed Jan 11 09:56:04 2023 +0000
@@ -22,7 +22,7 @@
 PRV	3148	.	Y	T	.	PASS	DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=1324;ALT_RV=264;ALT_QUAL=36;AF=0.77563
 PRV	3148	.	Y	C	.	PASS	DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=381;ALT_RV=75;ALT_QUAL=36;AF=0.223199
 PRV	3295	.	A	G	.	PASS	DP=1040;REF_DP=1002;REF_RV=1002;REF_QUAL=35;ALT_DP=38;ALT_RV=38;ALT_QUAL=33;AF=0.0365385
-PRV	5680	.	C	T	.	PASS	DP=35;REF_DP=27;REF_RV=5;REF_QUAL=44;ALT_DP=8;ALT_RV=2;ALT_QUAL=46;AF=0.228571
+PRV	5680	.	C	T	.	PASS	DP=35;REF_DP=27;REF_RV=10;REF_QUAL=44;ALT_DP=8;ALT_RV=3;ALT_QUAL=46;AF=0.228571
 PRV	5723	.	T	G	.	FAIL	DP=32;REF_DP=31;REF_RV=31;REF_QUAL=35;ALT_DP=1;ALT_RV=1;ALT_QUAL=21;AF=0.03125
 PRV	6201	.	A	G	.	FAIL	DP=12;REF_DP=10;REF_RV=0;REF_QUAL=35;ALT_DP=2;ALT_RV=0;ALT_QUAL=38;AF=0.166667
 PRV	6211	.	T	C	.	FAIL	DP=9;REF_DP=8;REF_RV=0;REF_QUAL=36;ALT_DP=1;ALT_RV=0;ALT_QUAL=35;AF=0.111111
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/Z52_a_annotated.tsv	Wed Jan 11 09:56:04 2023 +0000
@@ -0,0 +1,17 @@
+REGION	POS	REF	ALT	REF_DP	REF_RV	REF_QUAL	ALT_DP	ALT_RV	ALT_QUAL	ALT_FREQ	TOTAL_DP	PVAL	PASS	GFF_FEATURE	REF_CODON	REF_AA	ALT_CODON	ALT_AA
+PRV	350	A	T	101	101	36	5	5	35	0.0471698	106	0.0304989	FALSE	cds-YP_002790881.1	AAA	K	TAA	*
+PRV	722	C	+A	280	234	36	9	0	20	0.0319149	282	0.0349042	FALSE	NA	NA	NA	NA	NA
+PRV	1682	C	T	1097	984	37	34	33	37	0.0300088	1133	7.79053e-10	TRUE	cds-YP_002790881.1	CTG	L	TTG	L
+PRV	1965	T	G	302	113	37	63	25	37	0.172603	365	4.41891e-21	TRUE	cds-YP_002790881.1	GTT	V	GGT	G
+PRV	2702	A	G	31	31	36	1	1	23	0.03125	32	0.507937	FALSE	cds-YP_002790881.1	AGA	R	GGA	G
+PRV	2781	T	G	354	70	37	48	8	36	0.117647	408	4.33605e-16	TRUE	cds-YP_002790881.1	GTG	V	GGG	G
+PRV	2922	C	T	264	0	36	11	0	36	0.04	275	0.000440953	TRUE	cds-YP_002790881.1	ACT	T	ATT	I
+PRV	3148	Y	T	0	0	0	1324	264	36	0.77563	1707	0	TRUE	cds-YP_002790881.1	GAY	X	GAT	D
+PRV	3148	Y	C	0	0	0	381	75	36	0.223199	1707	0	TRUE	cds-YP_002790881.1	GAY	X	GAC	D
+PRV	3295	A	G	1002	1002	35	38	38	33	0.0365385	1040	4.30837e-11	TRUE	cds-YP_002790881.1	GCA	A	GCG	A
+PRV	5680	C	T	27	10	44	8	3	46	0.228571	35	0.000596701	TRUE	cds-YP_002790881.1	TTC	F	TTT	F
+PRV	5723	T	G	31	31	35	1	1	21	0.03125	32	0.507937	FALSE	cds-YP_002790881.1	TGA	*	GGA	G
+PRV	6201	A	G	10	0	35	2	0	38	0.166667	12	0.26087	FALSE	cds-YP_002790881.1	GAA	E	GGA	G
+PRV	6211	T	C	8	0	36	1	0	35	0.111111	9	0.5	FALSE	cds-YP_002790881.1	TGT	C	TGC	C
+PRV	7916	C	T	351	289	36	81	78	37	0.1875	432	5.39655e-27	TRUE	cds-YP_002790881.1	CAG	Q	TAG	*
+PRV	9713	C	T	374	0	37	13	0	35	0.0335917	387	0.00010474	TRUE	cds-YP_002790881.1	CTT	L	TTT	F
--- a/test-data/zika/Z52_a_pass.vcf	Wed Jul 13 15:20:33 2022 +0000
+++ b/test-data/zika/Z52_a_pass.vcf	Wed Jan 11 09:56:04 2023 +0000
@@ -19,6 +19,6 @@
 PRV	3148	.	Y	T	.	PASS	DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=1324;ALT_RV=264;ALT_QUAL=36;AF=0.77563
 PRV	3148	.	Y	C	.	PASS	DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=381;ALT_RV=75;ALT_QUAL=36;AF=0.223199
 PRV	3295	.	A	G	.	PASS	DP=1040;REF_DP=1002;REF_RV=1002;REF_QUAL=35;ALT_DP=38;ALT_RV=38;ALT_QUAL=33;AF=0.0365385
-PRV	5680	.	C	T	.	PASS	DP=35;REF_DP=27;REF_RV=5;REF_QUAL=44;ALT_DP=8;ALT_RV=2;ALT_QUAL=46;AF=0.228571
+PRV	5680	.	C	T	.	PASS	DP=35;REF_DP=27;REF_RV=10;REF_QUAL=44;ALT_DP=8;ALT_RV=3;ALT_QUAL=46;AF=0.228571
 PRV	7916	.	C	T	.	PASS	DP=432;REF_DP=351;REF_RV=289;REF_QUAL=36;ALT_DP=81;ALT_RV=78;ALT_QUAL=37;AF=0.1875
 PRV	9713	.	C	T	.	PASS	DP=387;REF_DP=374;REF_RV=0;REF_QUAL=37;ALT_DP=13;ALT_RV=0;ALT_QUAL=35;AF=0.0335917
Binary file test-data/zika/Z52_b.sorted.bam.bai has changed
Binary file test-data/zika/Z52_b.trimmed.sorted.bam.bai has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/zika/db/PRV.gff	Wed Jan 11 09:56:04 2023 +0000
@@ -0,0 +1,27 @@
+##gff-version 3
+#!gff-spec-version 1.21
+#!processor NCBI annotwriter
+#!genome-build ViralProj36615
+#!genome-build-accession NCBI_Assembly:GCF_000882815.3
+##sequence-region NC_012532.1 1 10794
+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=64320
+NC_012532.1	RefSeq	region	1	10794	.	+	.	ID=NC_012532.1:1..10794;Dbxref=taxon:64320;country=Uganda;gbkey=Src;genome=genomic;mol_type=genomic RNA;nat-host=sentinel monkey;note=mosquito-borne flavivirus;strain=MR 766
+NC_012532.1	RefSeq	five_prime_UTR	1	106	.	+	.	ID=id-NC_012532.1:1..106;gbkey=5'UTR
+NC_012532.1	RefSeq	gene	107	10366	.	+	.	ID=gene-ZIKV_gp1;Dbxref=GeneID:7751225;Name=POLY;gbkey=Gene;gene=POLY;gene_biotype=protein_coding;locus_tag=ZIKV_gp1
+NC_012532.1	RefSeq	CDS	107	10366	.	+	0	ID=cds-YP_002790881.1;Parent=gene-ZIKV_gp1;Dbxref=Genbank:YP_002790881.1,GeneID:7751225;Name=YP_002790881.1;gbkey=CDS;gene=POLY;locus_tag=ZIKV_gp1;product=polyprotein;protein_id=YP_002790881.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	107	472	.	+	.	ID=id-YP_002790881.1:1..122;Parent=cds-YP_002790881.1;gbkey=Prot;product=anchored capsid protein ancC;protein_id=YP_009227206.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	107	418	.	+	.	ID=id-YP_002790881.1:1..104;Parent=cds-YP_002790881.1;gbkey=Prot;product=capsid protein C;protein_id=YP_009227196.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	473	976	.	+	.	ID=id-YP_002790881.1:123..290;Parent=cds-YP_002790881.1;gbkey=Prot;product=membrane glycoprotein precursor prM;protein_id=YP_009227197.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	473	751	.	+	.	ID=id-YP_002790881.1:123..215;Parent=cds-YP_002790881.1;gbkey=Prot;product=protein pr;protein_id=YP_009227207.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	752	976	.	+	.	ID=id-YP_002790881.1:216..290;Parent=cds-YP_002790881.1;gbkey=Prot;product=membrane glycoprotein M;protein_id=YP_009227208.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	977	2476	.	+	.	ID=id-YP_002790881.1:291..790;Parent=cds-YP_002790881.1;gbkey=Prot;product=envelope protein E;protein_id=YP_009227198.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	2477	3532	.	+	.	ID=id-YP_002790881.1:791..1142;Parent=cds-YP_002790881.1;gbkey=Prot;product=nonstructural protein NS1;protein_id=YP_009227199.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	3533	4210	.	+	.	ID=id-YP_002790881.1:1143..1368;Parent=cds-YP_002790881.1;gbkey=Prot;product=nonstructural protein NS2A;protein_id=YP_009227200.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	4211	4600	.	+	.	ID=id-YP_002790881.1:1369..1498;Parent=cds-YP_002790881.1;gbkey=Prot;product=nonstructural protein NS2B;protein_id=YP_009227201.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	4601	6451	.	+	.	ID=id-YP_002790881.1:1499..2115;Parent=cds-YP_002790881.1;gbkey=Prot;product=nonstructural protein NS3;protein_id=YP_009227202.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	6452	6832	.	+	.	ID=id-YP_002790881.1:2116..2242;Parent=cds-YP_002790881.1;gbkey=Prot;product=nonstructural protein NS4A;protein_id=YP_009227203.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	6833	6901	.	+	.	ID=id-YP_002790881.1:2243..2265;Parent=cds-YP_002790881.1;gbkey=Prot;product=protein 2K;protein_id=YP_009227209.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	6902	7654	.	+	.	ID=id-YP_002790881.1:2266..2516;Parent=cds-YP_002790881.1;gbkey=Prot;product=nonstructural protein NS4B;protein_id=YP_009227204.1
+NC_012532.1	RefSeq	mature_protein_region_of_CDS	7655	10363	.	+	.	ID=id-YP_002790881.1:2517..3419;Parent=cds-YP_002790881.1;gbkey=Prot;product=RNA-dependent RNA polymerase NS5;protein_id=YP_009227205.1
+NC_012532.1	RefSeq	three_prime_UTR	10367	10794	.	+	.	ID=id-NC_012532.1:10367..10794;gbkey=3'UTR
+###
--- a/test-data/zika/primer_mismatchers_indices.txt	Wed Jul 13 15:20:33 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-400_18_out_L**	400_23_out_R	400_32_out_L
\ No newline at end of file