# HG changeset patch
# User nml
# Date 1492713218 14400
# Node ID 13632190a0ffb220f0e7842122832297b9cbbbe7
# Parent  9d7e381dfa5af865e1b06983639aad31e460fc47
planemo upload commit c190273bbf3bfd1efb6e14135601d746b748daab

diff -r 9d7e381dfa5a -r 13632190a0ff sistr_cmd.xml
--- a/sistr_cmd.xml	Fri Mar 03 14:31:21 2017 -0500
+++ b/sistr_cmd.xml	Thu Apr 20 14:33:38 2017 -0400
@@ -1,9 +1,9 @@
-<tool id="sistr_cmd" name="sistr_cmd" version="0.3.4">
+<tool id="sistr_cmd" name="sistr_cmd" version="0.3.6">
   <description>
     Salmonella In Silico Typing Resource commandline tool for serovar prediction
   </description>
   <requirements>
-    <requirement type="package" version="0.3.4">sistr_cmd</requirement>
+    <requirement type="package" version="0.3.6">sistr_cmd</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" />
@@ -25,6 +25,8 @@
     --threads "\${GALAXY_SLOTS:-1}"
     -T "\${TMPDIR:-/tmp}"
     $keep_tmp
+    $full_output
+    $report_blast_results
     $verbosity
   ]]></command>
   <inputs>
@@ -84,6 +86,22 @@
       label="Basic QC of results"
       />
     <param 
+      name="report_blast_results"
+      type="boolean"
+      checked="false"
+      truevalue="--report-blast-results"
+      falsevalue=""
+      label="Report all blastn results from antigen search"
+      />
+    <param 
+      name="full_output"
+      type="boolean"
+      checked="false"
+      truevalue="--full-output"
+      falsevalue=""
+      label="Report detailed results"
+      />
+    <param 
       name="keep_tmp"
       type="boolean"
       checked="false"
@@ -172,7 +190,7 @@
           <has_text text="Typhi" />
           <has_text text="enterica" />
           <has_text text="-:-:-" />
-          <has_n_columns n="19" />
+          <has_n_columns n="21" />
         </assert_contents>
       </output>
       <output 
@@ -206,7 +224,6 @@
           <has_text text="enterica" />
           <has_text text="1,4,[5],12" />
           <has_text text="PASS" />
-          <has_text text="2375035975"/>
           <has_n_columns n="21" />
         </assert_contents>
       </output>
@@ -241,7 +258,6 @@
           <has_text text="enterica" />
           <has_text text="1,4,[5],12" />
           <has_text text="PASS" />
-          <has_text text="2375035975"/>
           <has_n_columns n="21" />
         </assert_contents>
       </output>
@@ -258,7 +274,8 @@
 Usage::
 
     usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT]
-                     [-o OUTPUT_PREDICTION] [-p CGMLST_PROFILES]
+                     [-o OUTPUT_PREDICTION] [--full-output]
+                     [--report-blast-results] [-p CGMLST_PROFILES]
                      [-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K]
                      [--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS]
                      [-v] [-V]
@@ -288,6 +305,9 @@
                             Output format (json, csv, pickle)
       -o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION
                             SISTR serovar prediction output path
+      --full-output         Produce full detailed output
+      --report-blast-results
+                            Report blastn results for each antigen gene
       -p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES
                             Output CSV file destination for cgMLST allelic
                             profiles
diff -r 9d7e381dfa5a -r 13632190a0ff test-data/sistr-results.tab
--- a/test-data/sistr-results.tab	Fri Mar 03 14:31:21 2017 -0500
+++ b/test-data/sistr-results.tab	Thu Apr 20 14:33:38 2017 -0400
@@ -1,2 +1,2 @@
-cgmlst_distance	cgmlst_genome_match	cgmlst_matching_alleles	cgmlst_subspecies	fasta_filepath	genome	h1	h2	mash_distance	mash_genome	mash_match	mash_serovar	o_antigen	qc_messages	qc_status	serogroup	serovar	serovar_antigen	serovar_cgmlst
-0.827272727273	73530	57	enterica	/mnt/ssd240/work/repos/galaxy_tools/tools/sistr_cmd/test-data/AE014613-699860.fasta	AE014613-699860	-	-	0.0637124	60369	151	Typhi	-	FAIL: Large number of cgMLST330 loci missing (n=272 > 30) | FAIL: Wzx/Wzy genes missing. Cannot determine O-antigen group/serogroup. Cannot accurately predict serovar from antigen genes. | WARNING: H1 antigen gene (fliC) missing. Cannot determine H1 antigen. Cannot accurately predict serovar from antigen genes. | WARNING: Input genome size (699860 bp) not within expected range of 4000000-6000000 (bp) for Salmonella | WARNING: Only matched 57 cgMLST330 loci. Min threshold for confident serovar prediction from cgMLST is 297.0	FAIL	-	-:-:-	-:-:-	Typhi
+cgmlst_ST	cgmlst_distance	cgmlst_genome_match	cgmlst_matching_alleles	cgmlst_subspecies	fasta_filepath	genome	h1	h2	mash_distance	mash_genome	mash_match	mash_serovar	mash_subspecies	o_antigen	qc_messages	qc_status	serogroup	serovar	serovar_antigen	serovar_cgmlst
+	0.8272727272727273	73530	57	enterica	/mnt/ssd240/work/repos/galaxy_tools/tools/sistr_cmd/test-data/AE014613-699860.fasta	AE014613-699860	-	-	0.0637124	60369	151	Typhi		-	FAIL: Large number of cgMLST330 loci missing (n=272 > 30) | FAIL: Wzx/Wzy genes missing. Cannot determine O-antigen group/serogroup. Cannot accurately predict serovar from antigen genes. | WARNING: H1 antigen gene (fliC) missing. Cannot determine H1 antigen. Cannot accurately predict serovar from antigen genes. | WARNING: Input genome size (699860 bp) not within expected range of 4000000-6000000 (bp) for Salmonella | WARNING: Only matched 57 cgMLST330 loci. Min threshold for confident serovar prediction from cgMLST is 297.0	FAIL	-	-:-:-	-:-:-	Typhi