V1.11.4+galaxy0.2.7 (#27)

* bug fix for instrument types spectral matching

* added unit test for instrumentTypes

Author: Tomnl

README.rst

@@ -58,6 +58,10 @@ Authors, contributors & contacts
 
 Changes
 -------------------------
+v1.11.4-galaxy0.2.7
+  - submitted to test toolshed (20190927)
+  - Bug fix for spectralMatching choice of instrument types
+
 v1.11.4-galaxy0.2.6:
   - submitted to test toolshed (20190924)
   - Bug fix for createAnnotation database local path

tools/msPurity/macros.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.11.4</token>
-    <token name="@GALAXY_TOOL_VERSION@">0.2.6</token>
+    <token name="@GALAXY_TOOL_VERSION@">0.2.7</token>
 
     <xml name="requirements">
         <requirements>

tools/msPurity/spectralMatching.xml

@@ -103,30 +103,30 @@
 
             #if $Query.q_filters.q_sources_cond.q_sources_bool
               --q_sources=$Query.q_filters.q_sources_cond.q_sources
-              --q_sourcesUser=$Query.q_filters.q_sources_cond.q_sourcesUser
+              --q_sourcesUser="$Query.q_filters.q_sources_cond.q_sourcesUser"
             #end if
 
             #if $Library.l_filters.l_sources_cond.l_sources_bool
               --l_sources=$Library.l_filters.l_sources_cond.l_sources
-              --l_sourcesUser=$Library.l_filters.l_sources_cond.l_sourcesUser
+              --l_sourcesUser="$Library.l_filters.l_sources_cond.l_sourcesUser"
             #end if
 
             #if $Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes_bool
-              --q_instrumentTypes=$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes
-              --q_instrumentTypesUser=$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser
+              --q_instrumentTypes="$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes"
+              --q_instrumentTypesUser="$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser"
             #end if
 
             #if $Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes_bool
-              --l_instrumentTypes=$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes
-              --l_instrumentTypesUser=$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser
+              --l_instrumentTypes="$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes"
+              --l_instrumentTypesUser="$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser"
             #end if
 
             #if $Query.q_filters.q_instruments_cond.q_instruments_bool
-              --q_instruments=$Query.q_filters.q_instruments_cond.q_instruments
+              --q_instruments="$Query.q_filters.q_instruments_cond.q_instruments"
             #end if
 
             #if $Library.l_filters.l_instruments_cond.l_instruments_bool
-              --l_instruments=$Library.l_filters.l_instruments_cond.l_instruments
+              --l_instruments="$Library.l_filters.l_instruments_cond.l_instruments"
             #end if
 
             #if $Query.q_filters.q_spectraTypes_cond.q_spectraTypes_bool
@@ -251,6 +251,8 @@
     </outputs>
     <tests>
         <test>
+
+
             <param name="q_dbPth" value="createDatabase_output.sqlite" />
 	    <param name="l_dbPth_select" value="userdb" />
             <param name="l_dbPth" value="PR100037.sqlite" />
@@ -263,6 +265,23 @@
             <output name="matches" file="spectralMatching_xcms_matched_results.tsv" />
             <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching.sqlite" ftype="sqlite" compare="sim_size"/>
         </test>
+        <test>
+            <param name="l_instrumentTypes_bool" value="true" />
+            <param name="q_dbPth" value="createDatabase_output.sqlite" />
+	    <param name="l_dbPth_select" value="userdb" />
+            <param name="l_dbPth" value="PR100037.sqlite" />
+
+            <param name="q_xcmsGroups_bool" value="true" />
+            <param name="l_accessions_bool" value="true" />
+            <param name="q_xcmsGroups" value="14" />
+            <param name="l_accessions" value="PR100037" />
+
+            <output name="xcms_matches" file="spectralMatching_matched_results_instrumentTypes.tsv" />
+            <output name="matches" file="spectralMatching_xcms_matched_results_instrumentTypes.tsv" />
+            <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite" ftype="sqlite" compare="sim_size"/>
+        </test>
+
+
     </tests>
 
 

tools/msPurity/test-data/spectralMatching_db_with_spectral_matching.sqlite

@@ -0,0 +1,3 @@
+"pid"	"grpid"	"mz"	"mzmin"	"mzmax"	"rt"	"rtmin"	"rtmax"	"npeaks"	"sample"	"LCMSMS_2"	"LCMSMS_1"	"LCMS_2"	"LCMS_1"	"grp_name"	"lpid"	"mid"	"dpc"	"rdpc"	"cdpc"	"mcount"	"allcount"	"mpercent"	"library_rt"	"query_rt"	"rtdiff"	"library_precursor_mz"	"query_precursor_mz"	"library_precursor_ion_purity"	"query_precursor_ion_purity"	"library_accession"	"library_precursor_type"	"library_entry_name"	"inchikey"	"library_source_name"	"library_compound_name"
+1663	14	113.035283604395	113.035156497997	113.03541992282	80.50932	77.16429	83.64567	4	4	88462324.9597518	92812020.095242	77298864.2688328	77198465.9156761	"M113T81"	56653	1	0.942265461847349	0.996860823822942	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"
+1664	14	113.035283604395	113.035156497997	113.03541992282	80.50932	77.16429	83.64567	4	4	88462324.9597518	92812020.095242	77298864.2688328	77198465.9156761	"M113T81"	56653	2	0.942265461847349	0.996860823822942	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"

tools/msPurity/test-data/spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite

@@ -0,0 +1,3 @@
+"lpid"	"qpid"	"mid"	"dpc"	"rdpc"	"cdpc"	"mcount"	"allcount"	"mpercent"	"library_rt"	"query_rt"	"rtdiff"	"library_precursor_mz"	"query_precursor_mz"	"library_precursor_ion_purity"	"query_precursor_ion_purity"	"library_accession"	"library_precursor_type"	"library_entry_name"	"inchikey"	"library_source_name"	"library_compound_name"
+56653	1663	1	0.942265461847349	0.996860823822942	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"
+56653	1664	2	0.942265461847349	0.996860823822942	0.753812369477879	1	4	0.25	NA	80.50932	NA	"113.03508"	113.035283604395	NA	1	"PR100037"	"[M+H]+"	"Uracil"	"ISAKRJDGNUQOIC-UHFFFAOYSA-N"	"massbank"	"Uracil"