Mercurial > repos > iuc > ivar_removereads

changeset 12:8c05afb547fa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
author iuc
date Mon, 13 Feb 2023 17:31:02 +0000
parents 7f1cfa4c0e32
children 6a1515bb0687
files ivar_removereads.xml macros.xml test-data/zika/Z52_a.tsv test-data/zika/Z52_a_annotated.tsv
diffstat 4 files changed, 49 insertions(+), 39 deletions(-) [+]
line wrap: on
line diff
--- a/ivar_removereads.xml	Wed Jan 11 09:56:04 2023 +0000
+++ b/ivar_removereads.xml	Mon Feb 13 17:31:02 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="ivar_removereads" name="ivar removereads" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
+<tool id="ivar_removereads" name="ivar removereads" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Remove reads from trimmed BAM file</description>
     <macros>
         <import>macros.xml</import>
@@ -60,9 +60,14 @@
                 <param name="computed" value="no"/>
                 <param name="amplicon_info" value="zika/db/pair_information.tsv"/>
             </conditional>
+            <assert_stdout>
+                <!-- check that primer pairs are picked up correctly
+                from the amplicon info file -->
+                <has_text text="400_18_out_L**&#009;400_18_out_R**&#009;400_23_out_L&#009;400_23_out_R&#009;400_32_out_L&#009;400_32_out_R"/>
+            </assert_stdout>
             <output name="output_bam" ftype="bam">
                 <assert_contents>
-                    <has_size value="3185672" delta="1000"/>
+                    <has_size value="3130923" delta="1000"/>
                 </assert_contents>
             </output>
         </test>
@@ -73,9 +78,14 @@
             <conditional name="amplicons">
                 <param name="computed" value="yes"/>
             </conditional>
+            <assert_stdout>
+                <!-- check that primer pairs are picked up correctly
+                from the autogenerated amplicon info file -->
+                <has_text text="400_18_out_L**&#009;400_18_out_R**&#009;400_23_out_L&#009;400_23_out_R&#009;400_32_out_L&#009;400_32_out_R"/>
+            </assert_stdout>
             <output name="output_bam" ftype="bam">
                 <assert_contents>
-                    <has_size value="3185672" delta="1000"/>
+                    <has_size value="3130923" delta="1000"/>
                 </assert_contents>
             </output>
         </test>
--- a/macros.xml	Wed Jan 11 09:56:04 2023 +0000
+++ b/macros.xml	Mon Feb 13 17:31:02 2023 +0000
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <macros>
-  <token name="@TOOL_VERSION@">1.3.1</token>
+  <token name="@TOOL_VERSION@">1.3.2</token>
   <token name="@PROFILE@">21.01</token>
   <xml name="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>
+      <requirement type="package" version="1.16.1">samtools</requirement>
       <yield/>
   </requirements>
   </xml>
--- a/test-data/zika/Z52_a.tsv	Wed Jan 11 09:56:04 2023 +0000
+++ b/test-data/zika/Z52_a.tsv	Mon Feb 13 17:31:02 2023 +0000
@@ -1,17 +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	NA	NA	NA	NA	NA
-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	NA	NA	NA	NA	NA
-PRV	1965	T	G	302	113	37	63	25	37	0.172603	365	4.41891e-21	TRUE	NA	NA	NA	NA	NA
-PRV	2702	A	G	31	31	36	1	1	23	0.03125	32	0.507937	FALSE	NA	NA	NA	NA	NA
-PRV	2781	T	G	354	70	37	48	8	36	0.117647	408	4.33605e-16	TRUE	NA	NA	NA	NA	NA
-PRV	2922	C	T	264	0	36	11	0	36	0.04	275	0.000440953	TRUE	NA	NA	NA	NA	NA
-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	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
-PRV	7916	C	T	351	289	36	81	78	37	0.1875	432	5.39655e-27	TRUE	NA	NA	NA	NA	NA
-PRV	9713	C	T	374	0	37	13	0	35	0.0335917	387	0.00010474	TRUE	NA	NA	NA	NA	NA
+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	POS_AA
+PRV	350	A	T	101	101	36	5	5	35	0.0471698	106	0.0304989	FALSE	NA	NA	NA	NA	NA	NA
+PRV	722	C	+A	280	234	36	9	0	20	0.0319149	282	0.0349042	FALSE	NA	NA	NA	NA	NA	NA
+PRV	1682	C	T	1097	984	37	34	33	37	0.0300088	1133	7.79053e-10	TRUE	NA	NA	NA	NA	NA	NA
+PRV	1965	T	G	302	113	37	63	25	37	0.172603	365	4.41891e-21	TRUE	NA	NA	NA	NA	NA	NA
+PRV	2702	A	G	31	31	36	1	1	23	0.03125	32	0.507937	FALSE	NA	NA	NA	NA	NA	NA
+PRV	2781	T	G	354	70	37	48	8	36	0.117647	408	4.33605e-16	TRUE	NA	NA	NA	NA	NA	NA
+PRV	2922	C	T	264	0	36	11	0	36	0.04	275	0.000440953	TRUE	NA	NA	NA	NA	NA	NA
+PRV	3148	Y	T	0	0	0	1324	264	36	0.77563	1707	0	TRUE	NA	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	NA
+PRV	3295	A	G	1002	1002	35	38	38	33	0.0365385	1040	4.30837e-11	TRUE	NA	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	NA
+PRV	5723	T	G	31	31	35	1	1	21	0.03125	32	0.507937	FALSE	NA	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	NA
+PRV	6211	T	C	8	0	36	1	0	35	0.111111	9	0.5	FALSE	NA	NA	NA	NA	NA	NA
+PRV	7916	C	T	351	289	36	81	78	37	0.1875	432	5.39655e-27	TRUE	NA	NA	NA	NA	NA	NA
+PRV	9713	C	T	374	0	37	13	0	35	0.0335917	387	0.00010474	TRUE	NA	NA	NA	NA	NA	NA
--- a/test-data/zika/Z52_a_annotated.tsv	Wed Jan 11 09:56:04 2023 +0000
+++ b/test-data/zika/Z52_a_annotated.tsv	Mon Feb 13 17:31:02 2023 +0000
@@ -1,17 +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
+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	POS_AA
+PRV	350	A	T	101	101	36	5	5	35	0.0471698	106	0.0304989	FALSE	POLY:cds-YP_002790881.1	AAA	K	TAA	*	82
+PRV	722	C	+A	280	234	36	9	0	20	0.0319149	282	0.0349042	FALSE	NA	NA	NA	NA	NA	NA
+PRV	1682	C	T	1097	984	37	34	33	37	0.0300088	1133	7.79053e-10	TRUE	POLY:cds-YP_002790881.1	CTG	L	TTG	L	526
+PRV	1965	T	G	302	113	37	63	25	37	0.172603	365	4.41891e-21	TRUE	POLY:cds-YP_002790881.1	GTT	V	GGT	G	620
+PRV	2702	A	G	31	31	36	1	1	23	0.03125	32	0.507937	FALSE	POLY:cds-YP_002790881.1	AGA	R	GGA	G	866
+PRV	2781	T	G	354	70	37	48	8	36	0.117647	408	4.33605e-16	TRUE	POLY:cds-YP_002790881.1	GTG	V	GGG	G	892
+PRV	2922	C	T	264	0	36	11	0	36	0.04	275	0.000440953	TRUE	POLY:cds-YP_002790881.1	ACT	T	ATT	I	939
+PRV	3148	Y	T	0	0	0	1324	264	36	0.77563	1707	0	TRUE	POLY:cds-YP_002790881.1	GAY	X	GAT	D	1014
+PRV	3148	Y	C	0	0	0	381	75	36	0.223199	1707	0	TRUE	POLY:cds-YP_002790881.1	GAY	X	GAC	D	1014
+PRV	3295	A	G	1002	1002	35	38	38	33	0.0365385	1040	4.30837e-11	TRUE	POLY:cds-YP_002790881.1	GCA	A	GCG	A	1063
+PRV	5680	C	T	27	10	44	8	3	46	0.228571	35	0.000596701	TRUE	POLY:cds-YP_002790881.1	TTC	F	TTT	F	1858
+PRV	5723	T	G	31	31	35	1	1	21	0.03125	32	0.507937	FALSE	POLY:cds-YP_002790881.1	TGA	*	GGA	G	1873
+PRV	6201	A	G	10	0	35	2	0	38	0.166667	12	0.26087	FALSE	POLY:cds-YP_002790881.1	GAA	E	GGA	G	2032
+PRV	6211	T	C	8	0	36	1	0	35	0.111111	9	0.5	FALSE	POLY:cds-YP_002790881.1	TGT	C	TGC	C	2035
+PRV	7916	C	T	351	289	36	81	78	37	0.1875	432	5.39655e-27	TRUE	POLY:cds-YP_002790881.1	CAG	Q	TAG	*	2604
+PRV	9713	C	T	374	0	37	13	0	35	0.0335917	387	0.00010474	TRUE	POLY:cds-YP_002790881.1	CTT	L	TTT	F	3203