# HG changeset patch
# User nml
# Date 1523038832 14400
# Node ID af59ac46292630ccca97cd78da261b0027ff2c4a
# Parent  5a42e475436e9561755537d4e0904ac57bfb7e70
planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4fee4519135f7677cf50f721cf1ad7a7335ad66d-dirty

diff -r 5a42e475436e -r af59ac462926 bio_hansel.xml
--- a/bio_hansel.xml	Thu Feb 22 12:21:08 2018 -0500
+++ b/bio_hansel.xml	Fri Apr 06 14:20:32 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="bio_hansel" name="Bio Hansel" version="1.2.1">
+<tool id="bio_hansel" name="Bio Hansel" version="1.3.0">
     <description>SNV Subtyping with genome assemblies or reads</description>
     <requirements>
-        <requirement type="package" version="1.2.0">bio_hansel</requirement>
+        <requirement type="package" version="1.3.0">bio_hansel</requirement>
         <requirement type="package" version="17.2.0">attrs</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
@@ -179,7 +179,7 @@
             <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/>
             <output name="results.tab">
                 <assert_contents>
-                    <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+qc_status\s+qc_message"/>
+                    <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+qc_status\s+qc_message"/>
                 </assert_contents>
             </output>
             <output name="match_results.tab">
@@ -200,7 +200,7 @@
             <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/>
             <output name="results.tab">
                 <assert_contents>
-                    <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path"/>
+                    <has_text_matching expression="sample\s+scheme\s+scheme_version\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_expected\s+n_tiles_matching_positive\s+n_tiles_matching_positive_expected\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_expected\s+file_path\s+avg_tile_coverage\s+qc_status\s+qc_message"/>
                 </assert_contents>
             </output>
             <output name="match_results.tab">
@@ -323,7 +323,7 @@
     <citations>
         <citation type="bibtex">@ARTICLE{a1,
             title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.},
-            author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Chad R. Laing, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash.},
+            author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash.},
             url = {https://github.com/phac-nml/bio_hansel}
             }
         }</citation>