Mercurial > repos > nml > refseq_masher

changeset 2:1ec42f033bb4 draft default tip

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"planemo upload for repository https://github.com/phac-nml/refseq_masher commit 7176dbde2cafbf0858e806923a9f0bd3b2ebf7c0"
author nml
date Fri, 25 Jun 2021 23:38:54 +0000
parents 2c1cb37a3ffe
children
files contains.xml matches.xml test-data/SRR1203042_1-head4000-contains.tab test-data/SRR1203042_1-head4000-refseq_masher-matches-m2.tab
diffstat 4 files changed, 12 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/contains.xml	Wed May 08 09:15:56 2019 -0400
+++ b/contains.xml	Fri Jun 25 23:38:54 2021 +0000
@@ -3,7 +3,7 @@
     Find NCBI RefSeq Genomes contained in your sequences
   </description>
   <requirements>
-    <requirement type="package" version="0.1.1">refseq_masher</requirement>
+    <requirement type="package" version="0.1.2">refseq_masher</requirement>
   </requirements>
   <command detect_errors="exit_code">
 <![CDATA[
@@ -157,10 +157,11 @@
         <param name="min_identity" value="0.9"/>
         <param name="max_pvalue" value="0.01"/>
       </section>
-      <output name="output_path_tab"
-        value="SRR1203042_1-head4000-contains.tab"
-        ftype="tabular"
-        lines_diff="0">
+      <output name="output_path_tab" ftype="tabular">
+        <assert_contents>
+          <has_n_columns n="24" />
+          <has_n_lines n="6" />
+        </assert_contents>
       </output>
     </test>
   </tests>
--- a/matches.xml	Wed May 08 09:15:56 2019 -0400
+++ b/matches.xml	Fri Jun 25 23:38:54 2021 +0000
@@ -3,7 +3,7 @@
     Find closest matching NCBI RefSeq Genomes to your sequences
   </description>
   <requirements>
-    <requirement type="package" version="0.1.1">refseq_masher</requirement>
+    <requirement type="package" version="0.1.2">refseq_masher</requirement>
   </requirements>
   <command detect_errors="exit_code">
 <![CDATA[
@@ -168,10 +168,11 @@
         <param name="output_type" value="tab"/>
         <param name="min_kmer_threshold" value="2"/>
       </section>
-      <output name="output_path_tab"
-        value="SRR1203042_1-head4000-refseq_masher-matches-m2.tab"
-        ftype="tabular"
-        lines_diff="0">
+      <output name="output_path_tab" ftype="tabular">
+        <assert_contents>
+          <has_n_columns n="22" />
+          <has_n_lines n="2" />
+        </assert_contents>
       </output>
     </test>
   </tests>
--- a/test-data/SRR1203042_1-head4000-contains.tab	Wed May 08 09:15:56 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-sample	top_taxonomy_name	identity	shared_hashes	median_multiplicity	pvalue	full_taxonomy	taxonomic_subspecies	taxonomic_species	taxonomic_genus	taxonomic_family	taxonomic_order	taxonomic_class	taxonomic_phylum	taxonomic_superkingdom	subspecies	serovar	plasmid	bioproject	biosample	taxid	assembly_accession	match_id	match_comment
-SRR1203042-head4000	Salmonella enterica subsp. enterica serovar Typhimurium	0.934797	136/400	1	0.0	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Typhimurium	Salmonella enterica subsp. enterica	Salmonella enterica	Salmonella	Enterobacteriaceae	Enterobacterales	Gammaproteobacteria	Proteobacteria	Bacteria	enterica	Typhimurium		PRJNA188943		90371		./rcn/refseq-NG-90371-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Typhimurium.fna	
-SRR1203042-head4000	Salmonella enterica subsp. enterica serovar Typhimurium	0.934797	136/400	1	0.0	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Typhimurium	Salmonella enterica subsp. enterica	Salmonella enterica	Salmonella	Enterobacteriaceae	Enterobacterales	Gammaproteobacteria	Proteobacteria	Bacteria	enterica	Typhimurium		PRJNA188943		90371		./rcn/refseq-NR-90371-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Typhimurium.fna	
-SRR1203042-head4000	Salmonella enterica subsp. enterica serovar Choleraesuis	0.9326110000000001	131/400	1	0.0	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Choleraesuis	Salmonella enterica subsp. enterica	Salmonella enterica	Salmonella	Enterobacteriaceae	Enterobacterales	Gammaproteobacteria	Proteobacteria	Bacteria	enterica	Choleraesuis		PRJNA188943		119912		./rcn/refseq-NG-119912-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Choleraesuis.fna	
-SRR1203042-head4000	Salmonella enterica subsp. enterica serovar Choleraesuis	0.9326110000000001	131/400	1	0.0	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Choleraesuis	Salmonella enterica subsp. enterica	Salmonella enterica	Salmonella	Enterobacteriaceae	Enterobacterales	Gammaproteobacteria	Proteobacteria	Bacteria	enterica	Choleraesuis		PRJNA188943		119912		./rcn/refseq-NR-119912-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Choleraesuis.fna	
-SRR1203042-head4000	Atlantibacter hermannii	0.9224829999999999	110/400	1	0.0	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Atlantibacter; hermannii		Atlantibacter hermannii	Atlantibacter	Enterobacteriaceae	Enterobacterales	Gammaproteobacteria	Proteobacteria	Bacteria				PRJNA33175		565		./rcn/refseq-NR-565-PRJNA33175-.-.-.-Escherichia_hermannii.fna	
--- a/test-data/SRR1203042_1-head4000-refseq_masher-matches-m2.tab	Wed May 08 09:15:56 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-sample	top_taxonomy_name	distance	pvalue	matching	full_taxonomy	taxonomic_subspecies	taxonomic_species	taxonomic_genus	taxonomic_family	taxonomic_order	taxonomic_class	taxonomic_phylum	taxonomic_superkingdom	subspecies	serovar	plasmid	bioproject	biosample	taxid	assembly_accession	match_id
-SRR1203042-head4000	Salmonella enterica subsp. enterica serovar Typhimurium	0.141301	7.688639999999999e-108	22/400	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Typhimurium	Salmonella enterica subsp. enterica	Salmonella enterica	Salmonella	Enterobacteriaceae	Enterobacterales	Gammaproteobacteria	Proteobacteria	Bacteria	enterica	Typhimurium		PRJNA188943		90371		./rcn/refseq-NR-90371-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Typhimurium.fna