# HG changeset patch
# User galaxyp
# Date 1607197889 0
# Node ID 704cace078c42a32e643862a4c4a92ec9a843d8e
# Parent  1533239ed6f29561bc76bd1574fcfee6d3466c83
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3cafa1cc1ea87eb7a0dc0e7aae013780c3565178"

diff -r 1533239ed6f2 -r 704cace078c4 CometAdapter.xml
--- a/CometAdapter.xml	Fri Nov 06 19:19:46 2020 +0000
+++ b/CometAdapter.xml	Sat Dec 05 19:51:29 2020 +0000
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Identification]-->
-<tool id="CometAdapter" name="CometAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="CometAdapter" name="CometAdapter" version="@TOOL_VERSION@+galaxy0" profile="20.05">
   <description>Annotates MS/MS spectra using Comet.</description>
   <macros>
     <token name="@EXECUTABLE@">CometAdapter</token>
diff -r 1533239ed6f2 -r 704cace078c4 bump.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bump.json	Sat Dec 05 19:51:29 2020 +0000
@@ -0,0 +1,9 @@
+{
+"AssayGeneratorMetabo": 1,
+"LuciphorAdapter": 1,
+"MSFraggerAdapter": 1,
+"MSGFPlusAdapter": 1,
+"NovorAdapter": 1,
+"PSMFeatureExtractor": 1,
+"SiriusAdapter": 1
+}
diff -r 1533239ed6f2 -r 704cace078c4 generate.sh
--- a/generate.sh	Fri Nov 06 19:19:46 2020 +0000
+++ b/generate.sh	Sat Dec 05 19:51:29 2020 +0000
@@ -6,8 +6,8 @@
 ## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g')
 
 export tmp=$(mktemp -d)
+
 export CTDCONVERTER="$tmp/CTDConverter"
-
 ###############################################################################
 ## reset old data
 ###############################################################################
@@ -56,12 +56,14 @@
 find . -maxdepth 0 -name "[A-Z]*xml" -delete
 source $(dirname $(which conda))/../etc/profile.d/conda.sh
 conda activate $tmp/OpenMS$VERSION-env
-python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_  --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE > convert.out 2> convert.err
+python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_  --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE --bump-file bump.json > convert.out 2> convert.err
 if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi
 conda deactivate
 
 patch PepNovoAdapter.xml < PepNovoAdapter.patch
 patch OMSSAAdapter.xml < OMSSAAdapter.patch
+# this should not be necessary from 2.7 https://github.com/OpenMS/OpenMS/pull/5087
+patch PSMFeatureExtractor.xml < PSMFeatureExtractor.patch
 
 # https://github.com/OpenMS/OpenMS/pull/4984
 sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml
diff -r 1533239ed6f2 -r 704cace078c4 hardcoded_params.json
--- a/hardcoded_params.json	Fri Nov 06 19:19:46 2020 +0000
+++ b/hardcoded_params.json	Sat Dec 05 19:51:29 2020 +0000
@@ -122,6 +122,9 @@
 	"sirius:cores": [{
 		"value": "${GALAXY_SLOTS:-1}"
 	}],
+	"out_workspace_directory": [{
+		"value": "__SIRIUS_WORKSPACE__"
+	}],
 
 	"#": "hardcode the outer loop threads for OpenSwathWorkflow",
 	"outer_loop_threads": [{
diff -r 1533239ed6f2 -r 704cace078c4 macros.xml
--- a/macros.xml	Fri Nov 06 19:19:46 2020 +0000
+++ b/macros.xml	Sat Dec 05 19:51:29 2020 +0000
@@ -4,7 +4,6 @@
      add additional macro files using the m/macros parameter -->
 <macros>
   <token name="@TOOL_VERSION@">2.6</token>
-  <token name="@GALAXY_VERSION@">0</token>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">openms</requirement>
@@ -21,6 +20,7 @@
   <xml name="stdio">
     <stdio>
       <regex match="std::bad_alloc" level="fatal_oom" description="Could not allocate memory"/>
+      <regex match="OutOfMemoryError" level="fatal_oom" description="Could not allocate memory"/>
       <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
       <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
       <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/>
diff -r 1533239ed6f2 -r 704cace078c4 macros_autotest.xml
--- a/macros_autotest.xml	Fri Nov 06 19:19:46 2020 +0000
+++ b/macros_autotest.xml	Sat Dec 05 19:51:29 2020 +0000
@@ -126,7 +126,6 @@
       <param name="max_transitions" value="3"/>
       <param name="cosine_similarity_threshold" value="0.98"/>
       <param name="transition_threshold" value="5.0"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="deisotoping">
         <param name="use_deisotoper" value="false"/>
         <param name="fragment_tolerance" value="1.0"/>
@@ -195,7 +194,6 @@
       <param name="max_transitions" value="3"/>
       <param name="cosine_similarity_threshold" value="0.98"/>
       <param name="transition_threshold" value="5.0"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="deisotoping">
         <param name="use_deisotoper" value="false"/>
         <param name="fragment_tolerance" value="1.0"/>
@@ -264,7 +262,6 @@
       <param name="max_transitions" value="3"/>
       <param name="cosine_similarity_threshold" value="0.98"/>
       <param name="transition_threshold" value="5.0"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="deisotoping">
         <param name="use_deisotoper" value="false"/>
         <param name="fragment_tolerance" value="1.0"/>
@@ -333,7 +330,6 @@
       <param name="max_transitions" value="3"/>
       <param name="cosine_similarity_threshold" value="0.98"/>
       <param name="transition_threshold" value="5.0"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="deisotoping">
         <param name="use_deisotoper" value="false"/>
         <param name="fragment_tolerance" value="1.0"/>
@@ -402,7 +398,6 @@
       <param name="max_transitions" value="3"/>
       <param name="cosine_similarity_threshold" value="0.98"/>
       <param name="transition_threshold" value="5.0"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="deisotoping">
         <param name="use_deisotoper" value="false"/>
         <param name="fragment_tolerance" value="1.0"/>
@@ -471,7 +466,6 @@
       <param name="max_transitions" value="3"/>
       <param name="cosine_similarity_threshold" value="0.98"/>
       <param name="transition_threshold" value="3.0"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="deisotoping">
         <param name="use_deisotoper" value="false"/>
         <param name="fragment_tolerance" value="1.0"/>
@@ -540,7 +534,6 @@
       <param name="max_transitions" value="3"/>
       <param name="cosine_similarity_threshold" value="0.98"/>
       <param name="transition_threshold" value="3.0"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="deisotoping">
         <param name="use_deisotoper" value="false"/>
         <param name="fragment_tolerance" value="1.0"/>
@@ -609,7 +602,6 @@
       <param name="max_transitions" value="3"/>
       <param name="cosine_similarity_threshold" value="0.98"/>
       <param name="transition_threshold" value="3.0"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="deisotoping">
         <param name="use_deisotoper" value="false"/>
         <param name="fragment_tolerance" value="1.0"/>
@@ -678,7 +670,6 @@
       <param name="max_transitions" value="3"/>
       <param name="cosine_similarity_threshold" value="0.98"/>
       <param name="transition_threshold" value="3.0"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="deisotoping">
         <param name="use_deisotoper" value="false"/>
         <param name="fragment_tolerance" value="1.0"/>
@@ -24819,6 +24810,8 @@
       </output>
     </test>
   </xml>
+  <xml name="autotest_PSMFeatureExtractor_org">
+</xml>
   <xml name="autotest_PSMFeatureExtractor">
 </xml>
   <xml name="autotest_PTModel">
@@ -25472,7 +25465,6 @@
       </conditional>
       <param name="in" value="SiriusAdapter_1_input.mzML"/>
       <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="preprocessing">
         <param name="filter_by_num_masstraces" value="1"/>
         <param name="precursor_mz_tolerance" value="0.005"/>
@@ -25515,7 +25507,6 @@
       <param name="in" value="SiriusAdapter_2_input.mzML"/>
       <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
       <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="preprocessing">
         <param name="filter_by_num_masstraces" value="3"/>
         <param name="precursor_mz_tolerance" value="0.005"/>
@@ -25558,7 +25549,6 @@
       <param name="in" value="SiriusAdapter_3_input.mzML"/>
       <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
       <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="preprocessing">
         <param name="filter_by_num_masstraces" value="3"/>
         <param name="precursor_mz_tolerance" value="0.005"/>
@@ -25601,7 +25591,6 @@
       <param name="in" value="SiriusAdapter_3_input.mzML"/>
       <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
       <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="preprocessing">
         <param name="filter_by_num_masstraces" value="1"/>
         <param name="precursor_mz_tolerance" value="0.005"/>
@@ -25644,7 +25633,6 @@
       <param name="in" value="SiriusAdapter_4_input.mzML"/>
       <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
       <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="preprocessing">
         <param name="filter_by_num_masstraces" value="1"/>
         <param name="precursor_mz_tolerance" value="0.005"/>
@@ -25687,7 +25675,6 @@
       <param name="in" value="SiriusAdapter_4_input.mzML"/>
       <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
       <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="preprocessing">
         <param name="filter_by_num_masstraces" value="1"/>
         <param name="precursor_mz_tolerance" value="0.005"/>
@@ -25731,7 +25718,6 @@
       <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
       <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/>
       <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="out_workspace_directory" value=""/>
       <section name="preprocessing">
         <param name="filter_by_num_masstraces" value="1"/>
         <param name="precursor_mz_tolerance" value="0.005"/>
@@ -27202,4 +27188,4 @@
       </output>
     </test>
   </xml>
-<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/></macros>
+<xml name="autotest_RTPredict"/><xml name="autotest_InspectAdapter"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_PTPredict"/></macros>
diff -r 1533239ed6f2 -r 704cace078c4 macros_test.xml
--- a/macros_test.xml	Fri Nov 06 19:19:46 2020 +0000
+++ b/macros_test.xml	Sat Dec 05 19:51:29 2020 +0000
@@ -335,6 +335,7 @@
     <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
   </test>
 </xml>
+<!-- TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 -->
 <xml name="manutest_PSMFeatureExtractor">
   <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
     <param name="adv_opts_cond|test" value="true"/>
@@ -354,6 +355,13 @@
     <param name="out_type" value="mzid"/>
     <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>
   </test>
+  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
+    <param name="adv_opts_cond|test" value="true"/>
+    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
+    <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
+    <param name="out_type" value="idxml"/>
+    <output name="out" ftype="idxml" value="PSMFeatureExtractor_3.idXML" compare="sim_size" delta="500"/>
+  </test>
 </xml>
 <xml name="manutest_QCCalculator">
   <test expect_num_outputs="1"><!-- took test data from another test w mzML input -->
diff -r 1533239ed6f2 -r 704cace078c4 prepare_test_data_manual.sh
--- a/prepare_test_data_manual.sh	Fri Nov 06 19:19:46 2020 +0000
+++ b/prepare_test_data_manual.sh	Sat Dec 05 19:51:29 2020 +0000
@@ -86,10 +86,13 @@
 PhosphoScoring -in spectra.mzML -id MSGFPlusAdapter_1_out1.tmp -out PhosphoScoring.idxml > PhosphoScoring.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr
+# TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 
+PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out_type idXML -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr
+PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out_type mzid -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
+PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML -out_type idXML -out PSMFeatureExtractor_3.idXML > PSMFeatureExtractor_3.stdout 2> stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_3 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
 QCCalculator -test -in OpenPepXL_input.mzML -out QCCalculator1.qcML > QCCalculator_1.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'QCCalculator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
diff -r 1533239ed6f2 -r 704cace078c4 readme.md
--- a/readme.md	Fri Nov 06 19:19:46 2020 +0000
+++ b/readme.md	Sat Dec 05 19:51:29 2020 +0000
@@ -22,11 +22,14 @@
 
 Manual updates should only be done to
 
-- the `@GALAXY_VERSION@"` token in `macros.xml`
 - and the manually contributed tests in `macros_test.xml` (The goal is that all
   tools that do not have an automatically generated test are covered here)
 - the `hardcoded_params.json` files
 
+Wrapper versions are managed in `bump.json`. For tools listed in the file
+the wrapper version will be set accordingly and otherwise `0` is used. 
+For a major update of the tool version the bump file should be reset (to `{}`).
+
 In a few cases patches may be acceptable.
 
 Installation