From d2a184b3c6fa4085be6bb11595970cd77caea457 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sat, 11 Feb 2023 18:02:38 +0100
Subject: [PATCH] add --sanitize

and more minor changes
---
 tools/ont_fast5_api/compress_fast5.xml        | 24 ++++++++++++-------
 tools/ont_fast5_api/fast5_subset.xml          |  2 +-
 tools/ont_fast5_api/macros.xml                |  3 ++-
 tools/ont_fast5_api/multi_to_single_fast5.xml |  7 +++---
 tools/ont_fast5_api/single_to_multi_fast5.xml | 21 ++++++++--------
 5 files changed, 32 insertions(+), 25 deletions(-)

diff --git a/tools/ont_fast5_api/compress_fast5.xml b/tools/ont_fast5_api/compress_fast5.xml
index 2c5c576a453..c545ba69496 100644
--- a/tools/ont_fast5_api/compress_fast5.xml
+++ b/tools/ont_fast5_api/compress_fast5.xml
@@ -1,5 +1,4 @@
-<?xml version="1.0"?>
-<tool id="ont_fast5_api_compress_fast5" name="@TOOL_NAME@ Compress" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="ont_fast5_api_compress_fast5" name="@TOOL_NAME@ Compress" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>multi read file(s)</description>
     <macros>
         <import>macros.xml</import>
@@ -17,6 +16,7 @@ compress_fast5
 @INPUTPATH@
 @SAVEPATH@
 @COMPRESSION@
+$sanitize
 ## optional
 @THREADS@
 
@@ -28,6 +28,7 @@ compress_fast5
         <expand macro="compression">
             <option value="vbz" selected="true">VBZ</option>
         </expand>
+        <param type="boolean" argument="--sanitize" truevalue="--sanitize" falsevalue="" label="Remove optional groups" help="such as basecalling and modified base information"/>
     </inputs>
     <outputs>
         <expand macro="output"/>
@@ -35,8 +36,8 @@ compress_fast5
     <tests>
         <!-- #1 default -->
         <test expect_num_outputs="1">
-            <param name="input_path" value="multi.fast5.tar"/>
-            <output name="out_results">
+            <param name="input_path" value="multi.fast5.tar" ftype="fast5.tar"/>
+            <output name="out_results" ftype="fast5.tar">
                 <assert_contents>
                     <has_size value="40960"/>
                 </assert_contents>
@@ -44,23 +45,30 @@ compress_fast5
         </test>
         <!-- #2 -->
         <test expect_num_outputs="1">
-            <param name="input_path" value="multi.fast5.tar"/>
+            <param name="input_path" value="multi.fast5.tar" ftype="fast5.tar"/>
             <param name="compression" value="vbz_legacy_v0"/>
-            <output name="out_results">
+            <output name="out_results" ftype="fast5.tar">
                 <assert_contents>
                     <has_size value="40960"/>
                 </assert_contents>
             </output>
+            <assert_command>
+                <has_text text="--sanitize" negate="true"/>
+            </assert_command>
         </test>
         <!-- #3 -->
         <test expect_num_outputs="1">
-            <param name="input_path" value="multi.fast5.tar"/>
+            <param name="input_path" value="multi.fast5.tar" ftype="fast5.tar"/>
             <param name="compression" value="gzip"/>
-            <output name="out_results">
+            <param name="sanitize" value="true"/>
+            <output name="out_results" ftype="fast5.tar">
                 <assert_contents>
                     <has_size value="40960"/>
                 </assert_contents>
             </output>
+            <assert_command>
+                <has_text text="--sanitize"/>
+            </assert_command>
         </test>
     </tests>
     <help><![CDATA[
diff --git a/tools/ont_fast5_api/fast5_subset.xml b/tools/ont_fast5_api/fast5_subset.xml
index 08a30939079..1b5ff9cd733 100644
--- a/tools/ont_fast5_api/fast5_subset.xml
+++ b/tools/ont_fast5_api/fast5_subset.xml
@@ -1,4 +1,4 @@
-<tool id="ont_fast5_api_fast5_subset" name="@TOOL_NAME@ Subset" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="ont_fast5_api_fast5_subset" name="@TOOL_NAME@ Subset" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>of multi read file(s)</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/ont_fast5_api/macros.xml b/tools/ont_fast5_api/macros.xml
index 1c18c09872f..d67f645903a 100644
--- a/tools/ont_fast5_api/macros.xml
+++ b/tools/ont_fast5_api/macros.xml
@@ -1,6 +1,7 @@
 <macros>
     <token name="@TOOL_VERSION@">4.1.1</token>
-    <token name="@PROFILE@">20.05</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">22.01</token>
     <token name="@TOOL_NAME@">ont_fast5_api:</token>
     <xml name="requirements">
         <requirements>
diff --git a/tools/ont_fast5_api/multi_to_single_fast5.xml b/tools/ont_fast5_api/multi_to_single_fast5.xml
index 5e138618cb2..9987a3a0dc5 100644
--- a/tools/ont_fast5_api/multi_to_single_fast5.xml
+++ b/tools/ont_fast5_api/multi_to_single_fast5.xml
@@ -1,5 +1,4 @@
-<?xml version="1.0"?>
-<tool id="ont_fast5_api_multi_to_single_fast5" name="@TOOL_NAME@ Multi to single" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="ont_fast5_api_multi_to_single_fast5" name="@TOOL_NAME@ Multi to single" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>read file(s)</description>
     <macros>
         <import>macros.xml</import>
@@ -31,8 +30,8 @@ multi_to_single_fast5
     <tests>
         <!-- #1 default -->
         <test expect_num_outputs="1">
-            <param name="input_path" value="multi.fast5.tar"/>
-            <output name="out_results">
+            <param name="input_path" value="multi.fast5.tar" ftype="fast5.tar"/>
+            <output name="out_results" ftype="fast5.tar">
                 <assert_contents>
                     <has_size value="71680"/>
                 </assert_contents>
diff --git a/tools/ont_fast5_api/single_to_multi_fast5.xml b/tools/ont_fast5_api/single_to_multi_fast5.xml
index a90a8ffb6ab..2bc41ddcd9b 100644
--- a/tools/ont_fast5_api/single_to_multi_fast5.xml
+++ b/tools/ont_fast5_api/single_to_multi_fast5.xml
@@ -1,11 +1,10 @@
-<?xml version="1.0"?>
-<tool id="ont_fast5_api_single_to_multi_fast5" name="@TOOL_NAME@ Single to multi" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="ont_fast5_api_single_to_multi_fast5" name="@TOOL_NAME@ Single to multi" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>read file(s)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <version_command><![CDATA[single_to_multi -v]]></version_command>
+    <version_command><![CDATA[single_to_multi_fast5 -v]]></version_command>
     <command detect_errors="exit_code"><![CDATA[
 ## initialize
 @INITIALIZE@
@@ -38,8 +37,8 @@ single_to_multi_fast5
     <tests>
         <!-- #1 default -->
         <test expect_num_outputs="1">
-            <param name="input_path" value="single.fast5.tar"/>
-            <output name="out_results">
+            <param name="input_path" value="single.fast5.tar" ftype="fast5.tar"/>
+            <output name="out_results" ftype="fast5.tar">
                 <assert_contents>
                     <has_size value="40960"/>
                 </assert_contents>
@@ -47,10 +46,10 @@ single_to_multi_fast5
         </test>
         <!-- #2 -->
         <test expect_num_outputs="1">
-            <param name="input_path" value="single.fast5.tar"/>
+            <param name="input_path" value="single.fast5.tar" ftype="fast5.tar"/>
             <param name="batch_size" value="3"/>
             <param name="compression" value="vbz"/>
-            <output name="out_results">
+            <output name="out_results" ftype="fast5.tar">
                 <assert_contents>
                     <has_size value="51200"/>
                 </assert_contents>
@@ -58,9 +57,9 @@ single_to_multi_fast5
         </test>
         <!-- #3 -->
         <test expect_num_outputs="1">
-            <param name="input_path" value="single.fast5.tar"/>
+            <param name="input_path" value="single.fast5.tar" ftype="fast5.tar"/>
             <param name="compression" value="vbz_legacy_v0"/>
-            <output name="out_results">
+            <output name="out_results" ftype="fast5.tar">
                 <assert_contents>
                     <has_size value="40960"/>
                 </assert_contents>
@@ -68,9 +67,9 @@ single_to_multi_fast5
         </test>
         <!-- #4 -->
         <test expect_num_outputs="1">
-            <param name="input_path" value="single.fast5.tar"/>
+            <param name="input_path" value="single.fast5.tar" ftype="fast5.tar"/>
             <param name="compression" value="gzip"/>
-            <output name="out_results">
+            <output name="out_results" ftype="fast5.tar">
                 <assert_contents>
                     <has_size value="40960"/>
                 </assert_contents>