--- a/mqppep_preproc.xml	Wed Apr 13 19:48:01 2022 +0000
+++ b/mqppep_preproc.xml	Thu Jun 30 16:15:57 2022 +0000
@@ -2,20 +2,28 @@
   id="mqppep_preproc"
   name="MaxQuant Phosphopeptide Preprocessing"
   version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
-  python_template_version="3.5"
   profile="21.05"
   >
     <description>
-        Transform the output of MaxQuant for phosphoproteome-enriched samples to prepare it for statistical anlaysis.
+        Prep phosphoproteomic MaxQuant output for statistical anlaysis.
     </description>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <edam_topics>
+        <edam_topic>topic_0121</edam_topic><!-- Proteomics -->
+        <edam_topic>topic_3520</edam_topic><!-- Proteomics experiment-->
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_0338</edam_operation><!-- Sequence database search -->
+        <edam_operation>operation_0361</edam_operation><!-- Sequence annotation -->
+        <edam_operation>operation_3434</edam_operation><!-- Conversion -->
+        <edam_operation>operation_3436</edam_operation><!-- Aggregation -->
+    </edam_operations>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-      (
-        echo '--- localization-filter step:'
-      ) && (
+      echo '--- localization-filter step:'
+      && (
         Rscript '$__tool_directory__/MaxQuantProcessingScript.R'
         -i '$phosphoSites'
         #if $pst_py_selector == "y"
@@ -27,7 +35,7 @@
         --startCol '$startcol_script'
         --intervalCol $intervalCol
         --localProbCutoff $localProbCutoff
-        --collapse_func $collapseFunc
+        --collapse_func $collapse_func
         -o '$phosphoPepIntensities'
         --locProbCutoffGraph $locProbCutoffGraph
         --enrichGraph $enrichGraph
@@ -35,9 +43,9 @@
         --enrichGraph_svg $enrichGraph_svg
         --filtered_data $filteredData_tabular
         --quant_data $quantData_tabular
-      ) && (
-        echo '... end localization-filter.'
-      ) && (
+      ) &&
+      echo '... end localization-filter.'
+      && (
         echo '--- kinase-mapping step:'
       ) && (
         perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl'
@@ -57,11 +65,11 @@
         -O '$melted_phophopeptide_map'
         -D '$mqppep_output_sqlite'
         -s '$species'
-      ) && (
+      ) &&
         echo '... end kinase-mapping.'
-      ) && (
+      &&
         echo '--- merge-and-filter step:'
-      ) && (
+      && (
         python '$__tool_directory__/mqppep_mrgfltr.py'
         --phosphopeptides='$mapped_phophopeptides'
         --ppep_mapping_db='$mqppep_output_sqlite'
@@ -69,9 +77,8 @@
         --mrgfltr_tab='$preproc_tab'
         --mrgfltr_csv='$preproc_csv'
         --mrgfltr_sqlite='$preproc_sqlite'
-      ) && (
-        echo '... end merge-and-filter.'
       )
+      && echo '... end merge-and-filter.'
     ]]></command>
     <configfiles>
         <configfile name="phosphocol_script">$phosphoCol
@@ -82,11 +89,11 @@
     <inputs>
         <param name="phosphoSites" type="data" format="tabular"
                label="Phospho (STY)Sites.txt"
-               help="[phosphoSites] Tabular 'Phospho (STY)Sites.txt' produced by MaxQuant"
+               help="Tabular 'Phospho (STY)Sites.txt' produced by MaxQuant"
                />
         <param name="phosphoCol" type="text"
                label="pattern for column 'Number of Phospho (STY)'"
-               help="[phosphoCol] PERL-compatible regular expression matching header of column having number of 'Phospho (STY)'"
+               help="PERL-compatible regular expression matching header of column having number of 'Phospho (STY)'"
                value="^Number of Phospho [(]STY[)]$">
             <sanitizer>
                 <valid initial="string.printable">
@@ -96,7 +103,7 @@
         </param>
         <param name="startCol" type="text"
                label="pattern for first column of intensity values"
-               help="[startCol] PERL-compatible regular expression matching column header having first sample intensity"
+               help="PERL-compatible regular expression matching column header having first sample intensity"
                value="^Intensity[^_]">
             <sanitizer>
                 <valid initial="string.printable">
@@ -106,46 +113,46 @@
         </param>
         <param name="intervalCol" type="integer" value="1" min="1"
                label="Interval between the intensity column of samples"
-               help="[intervalCol] E.g., 1 if subsequent column is next sample; 2 if next sample is two columns away, etc."/>
+               help="E.g., 1 if subsequent column is next sample; 2 if next sample is two columns away, etc."/>
         <param name="pst_py_selector" type="select"
             label="Phosphopeptide enrichment type"
-            help="[enrichment] Were samples enriched for pS and pT, or were they enriched for pY instead?"
+            help="Were samples enriched for pS and pT, or were they enriched for pY instead?"
             >
             <option value="st" selected="true">pST</option>
             <option value="y">pY</option>
         </param>
-        <param name="collapseFunc" type="select"
+        <param name="collapse_func" type="select"
                label="Intensity merge function"
-               help="[collapseFunc] When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]"
+               help="When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]"
                >
             <option value="sum" selected="true">sum</option>
             <option value="mean">average</option>
         </param>
         <param name="localProbCutoff" type="float" value="0.75" min="0" max="1.0"
                label="Localization Probability Cutoff"
-               help="[localProbCutoff] See help below for an explanation."
+               help="See help below for an explanation."
                />
         <param name="merge_function" type="select" label="intensity merge-function"
-               help="[merge_function] Specifies how intensities for identical phosphosites should be merged">
+               help="Specifies how intensities for identical phosphosites should be merged">
             <option value="sum" selected="true">sum</option>
             <option value="average">average</option>
         </param>
         <param name="protein_fasta" type="data" format="fasta" label="UniProtKB/SwissProt FASTA database"
-               help="[protein_fasta] Sequence database; supply the same FASTA file as you supplied to by MaxQuant"
+               help="Sequence database; supply the same FASTA file as you supplied to by MaxQuant"
                />
         <param name="networkin" type="data" format="tabular" label="NetworKIN file"
-            help="[networkin] NetworKIN file; see help section below"/>
+            help="NetworKIN file; see help section below"/>
         <param name="p_sty_motifs" type="data" format="tabular" label="pSTY_Motifs file"
-            help="[p_sty_motifs] pS/pT/pY phosphorylation site motifs; see help section below"/>
+            help="pS/pT/pY phosphorylation site motifs; see help section below"/>
         <param name="psp_kinase_substrate" type="data" format="tabular" label="PSP_Kinase_Substrate_Dataset"
-            help="[psp_kinase_substrate] 'Kinase-substrate dataset'; see help section below"/>
+            help="'Kinase-substrate dataset'; see help section below"/>
         <param name="psp_regulatory_sites" type="data" format="tabular" label="PSP_Regulatory_sites"
-            help="[psp_regulatory_sites] 'Regulatory sites'; see help section below"/>
+            help="'Regulatory sites'; see help section below"/>
         <param name="species"
                type="text"
                value = "human"
                label="filter to limit PhosphoSitePlus records to indicated species"
-               help="[species] (field may be empty) [default: human]"
+               help="(field may be empty) [default: human].  If you supply this parameter, use the species indentifier seen as a suffix in UniProtKB"
                />
     </inputs>
     <outputs>
@@ -180,7 +187,7 @@
             <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/>
             <param name="startCol" value="^Intensity[^_]"/>
             <param name="intervalCol" value="1"/>
-            <param name="collapseFunc" value="sum"/>
+            <param name="collapse_func" value="sum"/>
             <param name="localProbCutoff" value="0.75"/>
             <param name="species" value="human"/>
 
@@ -200,36 +207,35 @@
                     <has_text text="cell cycle regulation" />
                     <has_text text="PPP2CA(INDUCES)" />
                     <has_text text="SNCA(DISRUPTS)" />
-                    <has_text text="Casein Kinase II substrate" />
-                    <has_text text="PKC kinase substrate" />
-                    <has_text text="PKCiota" />
-                    <has_text text="Csnk2a1" />
                     <has_text text="CDK7" />
                     <has_text text="CK1alpha" />
-                    <has_text text="CK2a2" />
                     <has_text text="CK2alpha" />
                     <has_text text="DNAPK" />
                     <has_text text="HIPK2" />
                     <has_text text="IKKalpha" />
                     <has_text text="PKCalpha" />
                     <has_text text="PKCbeta" />
+                    <has_text text="PKC" />
+                    <has_text text="CK2a2" />
+                    <has_text text="CK2alpha" />
+                    <has_text text="Csnk2a1" />
                 </assert_contents>
             </output>
 
             <output name="melted_phophopeptide_map">
                 <assert_contents>
-                    <has_text text="CDK7_NetworKIN" />
-                    <has_text text="CK1alpha_NetworKIN" />
-                    <has_text text="CK2a2_NetworKIN" />
-                    <has_text text="CK2alpha_NetworKIN" />
-                    <has_text text="DNAPK_NetworKIN" />
-                    <has_text text="HIPK2_NetworKIN" />
-                    <has_text text="IKKalpha_NetworKIN" />
-                    <has_text text="PKCalpha_NetworKIN" />
-                    <has_text text="PKCbeta_NetworKIN" />
-                    <has_text text="PKC kinase substrate motif" />
-                    <has_text text="Casein Kinase II substrate motif" />
-                    <has_text text="Csnk2a1_PhosphoSite" />
+                    <has_text text="CDK7" />
+                    <has_text text="CK1alpha" />
+                    <has_text text="CK2alpha" />
+                    <has_text text="DNAPK" />
+                    <has_text text="HIPK2" />
+                    <has_text text="IKKalpha" />
+                    <has_text text="PKCalpha" />
+                    <has_text text="PKCbeta" />
+                    <has_text text="PKC" />
+                    <has_text text="CK2a2" />
+                    <has_text text="CK2alpha" />
+                    <has_text text="Csnk2a1" />
                 </assert_contents>
             </output>
         </test>
@@ -246,7 +252,7 @@
             <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/>
             <param name="startCol" value="^Intensity[^_]"/>
             <param name="intervalCol" value="1"/>
-            <param name="collapseFunc" value="sum"/>
+            <param name="collapse_func" value="sum"/>
             <param name="localProbCutoff" value="0.75"/>
             <param name="species" value="human"/>
 
@@ -274,9 +280,9 @@
 
             <output name="melted_phophopeptide_map">
                 <assert_contents>
-                    <has_text text="Casein Kinase II substrate motif (HPRD)" />
-                    <has_text text="EPHA4_PhosphoSite" />
-                    <has_text text="EphA4_NetworKIN" />
+                    <has_text text="EphA6" />
+                    <has_text text="EPHA4" />
+                    <has_text text="EphA4" />
                 </assert_contents>
             </output>
         </test>
@@ -355,8 +361,11 @@
 
 **Authors**
 
+``Nicholas A. Graham``
+  (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script.
+
 ``Larry C. Cheng``
-  (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) wrote the original script.
+  (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) updated the original script.
 
 ``Arthur C. Eschenlauer``
   (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
@@ -482,10 +491,10 @@
 **Authors**
 
 ``Nicholas A. Graham``
-  (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) may have initiated the original script.
+  (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script.
 
 ``Larry C. Cheng``
-  (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) may have updated the original script.
+  (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) updated the original script.
 
 ``Arthur C. Eschenlauer``
   (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.