Mercurial > repos > nml > bio_hansel

diff bio_hansel.xml @ 7:af59ac462926 draft

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planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4fee4519135f7677cf50f721cf1ad7a7335ad66d-dirty
author nml
date Fri, 06 Apr 2018 14:20:32 -0400
parents 5a42e475436e
children e9fd173fc7ee
line wrap: on
line diff
--- 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>