Mercurial > repos > nml > staramr

changeset 9:61a3e97aa865 draft

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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 07b1134fbf48f0f94e6060b861651e1ab48cde71"
author nml
date Mon, 30 Sep 2019 12:45:02 -0400
parents da787fc8b740
children 7573a6c11c4d
files staramr_search.xml test-data/test1-detailed-summary.tsv test-data/test1-summary.tsv test-data/test2-summary.tsv test-data/test3-summary.tsv test-data/test4-summary.tsv test-data/test5-summary.tsv test-data/test6-summary.tsv
diffstat 8 files changed, 37 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/staramr_search.xml	Mon Jun 24 15:21:42 2019 -0400
+++ b/staramr_search.xml	Mon Sep 30 12:45:02 2019 -0400
@@ -1,7 +1,7 @@
 <tool id="staramr_search" name="staramr" version="@VERSION@">
     <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
     <macros>
-	    <token name="@VERSION@">0.5.1</token>
+	    <token name="@VERSION@">0.6.1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">staramr</requirement>
@@ -101,6 +101,7 @@
         </section>
     </inputs>
     <outputs>
+	<data format="tabular" name="mlst" label="${tool.name} on ${on_string}: mlst.tsv" />
         <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" />
         <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" />
         <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" />
@@ -117,7 +118,7 @@
     <tests>
         <test>
             <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
-            <param name="use_pointfinder" value="salmonella" />
+            <param name="use_pointfinder" value="salmonella" /> 
 
             <output name="summary" file="test1-summary.tsv" ftype="tabular" />
             <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" />
@@ -204,7 +205,21 @@
 Output
 ------
 
-There are 5 different output files produced by `staramr` as well as a collection of additional files.
+There are 6 different output files produced by `staramr` as well as a collection of additional files.
+
+mlst.tsv
+````````````````````
+
+A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line.
+
++------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
+| Isolate ID | Scheme       | Sequence Type                     | Locus 1    | Locus 2    | Locus 3    | Locus 4    | Locus 5    | Locus 6    | Locus 7    |
++============+==============+===================================+============+============+============+============+============+============+============+
+| SRR1952908 | senterica    | 11                                | aroC(5)    | dnaN(2)    | hemD(3)    | hisD(7)    | purE(6)    | sucA(6)    | thrA(11)   |
++------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+---+--------+
+| SRR1952926 | senterica    | 11                                | aroC(5)    | dnaN(2)    | hemD(3)    | hisD(7)    | purE(6)    | sucA(6)    | thrA(11)   |
++------------+--------------+-----------------------------------+------------+------------+------------+------------+------------+------------+------------+
+
 
 summary.tsv
 ```````````
@@ -336,7 +351,7 @@
 ::
 
     command_line                  = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
-    version                       = 0.5.1
+    version                       = 0.6.1
     start_time                    = 2019-04-25 16:01:32
     end_time                      = 2019-04-25 16:01:34
     total_minutes                 = 0.04
--- a/test-data/test1-detailed-summary.tsv	Mon Jun 24 15:21:42 2019 -0400
+++ b/test-data/test1-detailed-summary.tsv	Mon Sep 30 12:45:02 2019 -0400
@@ -1,5 +1,6 @@
-Isolate ID	Gene/Plasmid	Predicted Phenotype	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Accession	Data Type
-16S-rc_gyrA-rc_beta-lactam.fsa	None									Plasmid
-16S-rc_gyrA-rc_beta-lactam.fsa	16S_rrsD (C1065T)	spectinomycin	99.94	100.0	1544/1544	16S_rrsD	1604	61		Resistance
-16S-rc_gyrA-rc_beta-lactam.fsa	blaIMP-42	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	99.73	100.0	741/741	16S_rrsD	4381	5121	AB753456	Resistance
-16S-rc_gyrA-rc_beta-lactam.fsa	gyrA (A67P)	ciprofloxacin I/R, nalidixic acid	99.96	100.0	2637/2637	16S_rrsD	4317	1681		Resistance
+Isolate ID	Data	Data Type	Predicted Phenotype	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Accession
+16S-rc_gyrA-rc_beta-lactam.fsa	ST- (-)	MLST								
+16S-rc_gyrA-rc_beta-lactam.fsa	None	Plasmid								
+16S-rc_gyrA-rc_beta-lactam.fsa	16S_rrsD (C1065T)	Resistance	spectinomycin	99.94	100.0	1544/1544	16S_rrsD	1604	61	
+16S-rc_gyrA-rc_beta-lactam.fsa	blaIMP-42	Resistance	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	99.73	100.0	741/741	16S_rrsD	4381	5121	AB753456
+16S-rc_gyrA-rc_beta-lactam.fsa	gyrA (A67P)	Resistance	ciprofloxacin I/R, nalidixic acid	99.96	100.0	2637/2637	16S_rrsD	4317	1681	
--- a/test-data/test1-summary.tsv	Mon Jun 24 15:21:42 2019 -0400
+++ b/test-data/test1-summary.tsv	Mon Sep 30 12:45:02 2019 -0400
@@ -1,2 +1,2 @@
-Isolate ID	Genotype	Predicted Phenotype	Plasmid
-16S-rc_gyrA-rc_beta-lactam.fsa	16S_rrsD (C1065T), blaIMP-42, gyrA (A67P)	spectinomycin, ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem, ciprofloxacin I/R, nalidixic acid	None
+Isolate ID	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type
+16S-rc_gyrA-rc_beta-lactam.fsa	16S_rrsD (C1065T), blaIMP-42, gyrA (A67P)	spectinomycin, ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem, ciprofloxacin I/R, nalidixic acid	None	-	-
--- a/test-data/test2-summary.tsv	Mon Jun 24 15:21:42 2019 -0400
+++ b/test-data/test2-summary.tsv	Mon Sep 30 12:45:02 2019 -0400
@@ -1,2 +1,2 @@
-Isolate ID	Genotype	Predicted Phenotype	Plasmid
-16S-rc_gyrA-rc_beta-lactam.fsa	blaIMP-42	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	None
+Isolate ID	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type
+16S-rc_gyrA-rc_beta-lactam.fsa	blaIMP-42	ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem	None	-	-
--- a/test-data/test3-summary.tsv	Mon Jun 24 15:21:42 2019 -0400
+++ b/test-data/test3-summary.tsv	Mon Sep 30 12:45:02 2019 -0400
@@ -1,2 +1,2 @@
-Isolate ID	Genotype	Predicted Phenotype	Plasmid
-16S-rc_gyrA-rc_beta-lactam.fsa	None	Sensitive	None
+Isolate ID	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type
+16S-rc_gyrA-rc_beta-lactam.fsa	None	Sensitive	None	-	-
--- a/test-data/test4-summary.tsv	Mon Jun 24 15:21:42 2019 -0400
+++ b/test-data/test4-summary.tsv	Mon Sep 30 12:45:02 2019 -0400
@@ -1,2 +1,2 @@
-Isolate ID	Genotype	Predicted Phenotype	Plasmid
-16S_rc_gyrA_rc_beta-lactam_spaces__extra:characters_.fsa	None	Sensitive	None
+Isolate ID	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type
+16S_rc_gyrA_rc_beta-lactam_spaces__extra:characters_.fsa	None	Sensitive	None	-	-
--- a/test-data/test5-summary.tsv	Mon Jun 24 15:21:42 2019 -0400
+++ b/test-data/test5-summary.tsv	Mon Sep 30 12:45:02 2019 -0400
@@ -1,2 +1,2 @@
-Isolate ID	Genotype	Predicted Phenotype	Plasmid
-test-aminoglycoside.fsa	None	Sensitive	None
+Isolate ID	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type
+test-aminoglycoside.fsa	None	Sensitive	None	-	-
--- a/test-data/test6-summary.tsv	Mon Jun 24 15:21:42 2019 -0400
+++ b/test-data/test6-summary.tsv	Mon Sep 30 12:45:02 2019 -0400
@@ -1,2 +1,2 @@
-Isolate ID	Genotype	Predicted Phenotype	Plasmid
-test-aminoglycoside.fsa	aac(6')-Iaa	gentamicin	None
+Isolate ID	Genotype	Predicted Phenotype	Plasmid	Scheme	Sequence Type
+test-aminoglycoside.fsa	aac(6')-Iaa	gentamicin	None	-	-