diff picard_NormalizeFasta.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

--- a/picard_NormalizeFasta.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_NormalizeFasta.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,50 +1,46 @@
-<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <description>normalize fasta datasets</description>
-  <macros>
-    <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
-  </macros>
-  <expand macro="requirements" />
-  <command detect_errors="exit_code"><![CDATA[
+<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
+    <description>normalize fasta datasets</description>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
     @java_options@
 
     ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
     #import re
     #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
-    ln -f -s '$inputFile' '$escaped_element_identifier'.fa &&
-    picard
-    NormalizeFasta
+    ln -sf '$inputFile' '$escaped_element_identifier'.fa &&
+    
+    picard NormalizeFasta
 
-    INPUT='$escaped_element_identifier'.fa
-    OUTPUT="${outFile}"
-    LINE_LENGTH="${line_length}"
-    TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
+    --INPUT '$escaped_element_identifier'.fa
+    --OUTPUT '${outFile}'
+    --LINE_LENGTH '${line_length}'
+    --TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE '${truncate_sequence_names_at_whitespaces}'
 
-    QUIET=true
-    VERBOSITY=ERROR
+    --QUIET true
+    --VERBOSITY ERROR
 
   ]]></command>
-  <inputs>
-    <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" />
-    <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
-    <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
-  </inputs>
-
-  <outputs>
-    <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
-      <param name="line_length" value="40"/>
-      <param name="truncate_sequence_names_at_whitespaces" value="False"/>
-      <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
-    </test>
-  </tests>
-
-
-  <help>
+    <inputs>
+        <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset"/>
+        <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
+        <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
+            <param name="line_length" value="40"/>
+            <param name="truncate_sequence_names_at_whitespaces" value="False"/>
+            <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
+        </test>
+    </tests>
+    <help>
 
 **Purpose**
 
@@ -62,5 +58,5 @@
 @more_info@
 
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>