diff macros_autotest.xml @ 5:704cace078c4 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3cafa1cc1ea87eb7a0dc0e7aae013780c3565178"

--- 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>