initial cleanup

computational-metabolomics · Jun 11, 2024 · 7fb1c9b · 7fb1c9b
1 parent e3b1749
commit 7fb1c9b
Show file tree

Hide file tree

Showing 8 changed files with 5 additions and 177 deletions.
diff --git a/bioblend/install_dep.py b/bioblend/install_dep.py
diff --git a/conda_testing/DESCRIPTION b/conda_testing/DESCRIPTION
diff --git a/conda_testing/build.sh b/conda_testing/build.sh
diff --git a/conda_testing/meta.yaml b/conda_testing/meta.yaml
diff --git a/tools/msPurity/combineAnnotations.xml b/tools/msPurity/combineAnnotations.xml
@@ -115,7 +115,7 @@
             <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
 	    <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
              <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
-            <param name="beams_resultPth" value="combineAnnotations_input_beams.tsv" />
+            <param name="ms1_lookup_resultPth" value="combineAnnotations_input_beams.tsv" />
             <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
             <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" />
             <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/>

diff --git a/tools/msPurity/flagRemove.xml b/tools/msPurity/flagRemove.xml
@@ -158,10 +158,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="blank_flag.blank_flag" value="update" />
+
             <param name="xset_path" value="flagRemove_input.RData"/>
-
-            <param name="blank_flag.blank_flag" value="update" />
             <conditional name="blank_flag">
                 <param name="blank_flag"  value="update"/>
                 <param name="blank_class" value="KO" />

diff --git a/tools/msPurity/macros.xml b/tools/msPurity/macros.xml
@@ -1,14 +1,14 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.16.2</token>
-    <token name="@GALAXY_TOOL_VERSION@">1</token>
+    <token name="@TOOL_VERSION@">1.28.0</token>
+    <token name="@GALAXY_TOOL_VERSION@">2</token>
 
     <xml name="requirements">
         <requirements>
            <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement>
            <requirement type="package" version="1.46.0" >bioconductor-camera</requirement>
            <requirement type="package" version="3.12.0" >bioconductor-xcms</requirement>
-           <requirement type="package" version="1.16.0" >bioconductor-mspuritydata</requirement>
+           <requirement type="package" version="1.18.0" >bioconductor-mspuritydata</requirement>
            <requirement type="package" version="1.6.6">r-optparse</requirement>
            <requirement type="package" version="1.3.1">r-rpostgres</requirement>
            <requirement type="package" version="0.10.21">r-rmysql</requirement>

diff --git a/tools/utils/submit_to_mogi.xml b/tools/utils/submit_to_mogi.xml