add --sanitize

and more minor changes
galaxyproject · Feb 11, 2023 · d2a184b · d2a184b
1 parent 6d09f33
commit d2a184b
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Showing 5 changed files with 32 additions and 25 deletions.
diff --git 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@
 
@@ -28,39 +28,47 @@ 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"/>
     </outputs>
     <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>
             </output>
         </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
@@ -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
@@ -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
@@ -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
@@ -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@
@@ -38,39 +37,39 @@ 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>
             </output>
         </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>
             </output>
         </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>
             </output>
         </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>