From e38da08033af8f194c4a0d77d87980d7319890ce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <berenice.batut@gmail.com>
Date: Mon, 11 Mar 2024 13:16:19 +0100
Subject: [PATCH 1/2] Add bio.tools for peptideshaker

---
 tools/peptideshaker/fasta_cli.xml      | 3 ++-
 tools/peptideshaker/ident_params.xml   | 1 +
 tools/peptideshaker/macros_basic.xml   | 5 +++++
 tools/peptideshaker/peptide_shaker.xml | 1 +
 tools/peptideshaker/searchgui.xml      | 1 +
 5 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/tools/peptideshaker/fasta_cli.xml b/tools/peptideshaker/fasta_cli.xml
index 9c21a0fb1..652bc6ac9 100755
--- a/tools/peptideshaker/fasta_cli.xml
+++ b/tools/peptideshaker/fasta_cli.xml
@@ -9,8 +9,9 @@
     <macros>
         <import>macros_basic.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <requirements>
-	<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
+	    <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
diff --git a/tools/peptideshaker/ident_params.xml b/tools/peptideshaker/ident_params.xml
index 523de7d39..6aa1d749d 100755
--- a/tools/peptideshaker/ident_params.xml
+++ b/tools/peptideshaker/ident_params.xml
@@ -10,6 +10,7 @@
         <import>macros_basic.xml</import>
         <import>macros_modifications.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <requirements>
       	<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
     </requirements>
diff --git a/tools/peptideshaker/macros_basic.xml b/tools/peptideshaker/macros_basic.xml
index bf6317d2f..6a7540f9a 100755
--- a/tools/peptideshaker/macros_basic.xml
+++ b/tools/peptideshaker/macros_basic.xml
@@ -15,6 +15,11 @@
     <token name="@SEARCHGUI_VERSION_SUFFIX@">1</token>
     <token name="@PEPTIDESHAKER_VERSION@">2.0.33</token>
     <token name="@PEPTIDESHAKER_VERSION_SUFFIX@">1</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">peptideshaker</xref>
+        </xrefs>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1186/1471-2105-12-70</citation>
diff --git a/tools/peptideshaker/peptide_shaker.xml b/tools/peptideshaker/peptide_shaker.xml
index 695805a7c..b5ec26efe 100755
--- a/tools/peptideshaker/peptide_shaker.xml
+++ b/tools/peptideshaker/peptide_shaker.xml
@@ -11,6 +11,7 @@
         <import>macros_basic.xml</import>
         <import>macros_modifications.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <requirements>
         <requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement>
         <requirement type="package">unzip</requirement>
diff --git a/tools/peptideshaker/searchgui.xml b/tools/peptideshaker/searchgui.xml
index 3c3d08de9..8ac18c840 100755
--- a/tools/peptideshaker/searchgui.xml
+++ b/tools/peptideshaker/searchgui.xml
@@ -9,6 +9,7 @@
     <macros>
         <import>macros_basic.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <requirements>
         <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
         <requirement type="package" version="3.0">zip</requirement>

From 06c071462263ddc2d7a33b4660e0b3930d483bca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <berenice.batut@gmail.com>
Date: Mon, 18 Mar 2024 15:21:19 +0100
Subject: [PATCH 2/2] Try to fix linting

---
 tools/peptideshaker/fasta_cli.xml            |  4 +++-
 tools/peptideshaker/ident_params.xml         |  2 +-
 tools/peptideshaker/macros_modifications.xml |  3 +--
 tools/peptideshaker/peptide_shaker.xml       | 10 ++++++++--
 4 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/tools/peptideshaker/fasta_cli.xml b/tools/peptideshaker/fasta_cli.xml
index 652bc6ac9..16805ab0f 100755
--- a/tools/peptideshaker/fasta_cli.xml
+++ b/tools/peptideshaker/fasta_cli.xml
@@ -67,7 +67,9 @@
     <tests>
         <test>
             <param name="input_database" value="fastacli_searchgui_tinydb1.fasta" ftype="fasta"/>
-            <output name="input_database_concatenated_target_decoy" file="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" compare="sim_size" delta="1000" />
+            <output name="input_database_concatenated_target_decoy">
+                <discovered_dataset file="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" compare="sim_size" delta="1000"/>
+            </output>
         </test>
     </tests>
     <help>
diff --git a/tools/peptideshaker/ident_params.xml b/tools/peptideshaker/ident_params.xml
index 6aa1d749d..eef08aa2e 100755
--- a/tools/peptideshaker/ident_params.xml
+++ b/tools/peptideshaker/ident_params.xml
@@ -654,7 +654,7 @@
                             <option value="Trypsin">Trypsin</option>
                             <option value="Trypsin (no P rule)">Trypsin (no P rule)</option>
                             <option value="Arg-C">Arg-C</option>
-                            <option value="Arg-C (no P rule)">Arg-C</option>
+                            <option value="Arg-C (no P rule)">Arg-C (no P rule)</option>
                             <option value="Arg-N">Arg-N</option>
                             <option value="Glu-C">Glu-C</option>
                             <option value="Lys-C">Lys-C</option>
diff --git a/tools/peptideshaker/macros_modifications.xml b/tools/peptideshaker/macros_modifications.xml
index 0c709d352..41c16ca93 100644
--- a/tools/peptideshaker/macros_modifications.xml
+++ b/tools/peptideshaker/macros_modifications.xml
@@ -119,8 +119,6 @@
       <option value="Sulfation of T">Sulfation of T</option>
       <option value="Sulfation of Y">Sulfation of Y</option>
       <option value="S-nitrosylation">S-nitrosylation</option>
-      <option value="TMT 10-plex of K">TMT 10-plex of K</option>
-      <option value="TMT 10-plex of peptide N-term">TMT 10-plex of peptide N-term</option>
       <option value="TMT 2-plex of K">TMT 2-plex of K</option>
       <option value="TMT 2-plex of peptide N-term">TMT 2-plex of peptide N-term</option>
       <option value="TMT 6-plex of K">TMT 6-plex of K</option>
@@ -128,6 +126,7 @@
       <option value="TMT 6-plex of K+6">TMT 6-plex of K+6</option>
       <option value="TMT 6-plex of K+8">TMT 6-plex of K+8</option>
       <option value="TMT 6-plex of peptide N-term">TMT 6-plex of peptide N-term</option>
+      <option value="TMT 10-plex of K">TMT 10-plex of K</option>
       <option value="TMT 10-plex of K+4">TMT 10-plex of K+4</option>
       <option value="TMT 10-plex of K+6">TMT 10-plex of K+6</option>
       <option value="TMT 10-plex of K+8">TMT 10-plex of K+8</option>
diff --git a/tools/peptideshaker/peptide_shaker.xml b/tools/peptideshaker/peptide_shaker.xml
index b5ec26efe..6898a9361 100755
--- a/tools/peptideshaker/peptide_shaker.xml
+++ b/tools/peptideshaker/peptide_shaker.xml
@@ -295,7 +295,10 @@
         <section name="exporting_options" expanded="true" title="Exporting options" help="All different outputs PeptideShaker may produce">
 
             <conditional name="zip_conditional">
-                <param name="zip_output_boolean" type="boolean" truevalue="zip" falsevalue="separate" checked="false" label="Compress results into a single zip file" />
+                <param name="zip_output_boolean" type="select" label="Compress results into a single zip file">
+                    <option value="zip">Yes</option>
+                    <option value="separate" selected="true">No</option>
+                </param>
                 <when value="separate">
                     <param name="export_psdb" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports PeptideShakers‘ .psdb file" />
                 </when>
@@ -306,7 +309,10 @@
             </conditional>
 
             <conditional name="mzidentml_conditional">
-                <param name="mzidentml_creation" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Creates a mzIdentML file" />
+                <param name="mzidentml_creation" type="select" label="Creates a mzIdentML file">
+                    <option value="1">Yes</option>
+                    <option value="0">No</option>
+                </param>
                 <when value="1">
               	     <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in the mzIdentML file" />