diff fasta_interlacer.xml @ 22:58807b35777a draft

planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty

--- a/fasta_interlacer.xml	Thu Jul 27 09:46:13 2023 +0000
+++ b/fasta_interlacer.xml	Wed Aug 02 11:31:12 2023 +0000
@@ -1,33 +1,39 @@
+<tool id="fasta_interlacer" name="FASTA interlacer" version="1.0.0.3">
+    <description>Join pared reads into single file</description>
+    <required_files>
+        <include type="literal" path="fasta_interlacer.py"/>
+    </required_files>
+    <command>
+        python '$__tool_directory__'/fasta_interlacer.py -a $A -b $B -p $paired -x $single
+    </command>
 
-<tool id="fasta_interlacer" name="FASTA interlacer" version="1.0.0">
-<description> Join pared reads into single file </description>
-<command interpreter="python">
-fasta_interlacer.py -a $A -b $B -p $paired -x $single
-</command>
-
- <inputs>
-  <param format="fasta" type="data" name="A" label="Left-hand mates" />
-  <param format="fasta" type="data" name="B" label="Right-hand mates" />
- </inputs>
+    <inputs>
+        <param format="fasta" type="data" name="A" label="Left-hand mates"/>
+        <param format="fasta" type="data" name="B" label="Right-hand mates"/>
+    </inputs>
 
 
- <outputs>
-    <data format="fasta" name="paired" label="Interlaced paired reads from datasets ${A.hid} and ${B.hid} "/>
-   	<data format="fasta" name="single" label="Reads without corresponding mate from datasets ${A.hid} and ${B.hid}"/>
- </outputs>
+    <outputs>
+        <data format="fasta" name="paired"
+              label="Interlaced paired reads from datasets ${A.hid} and ${B.hid} "/>
+        <data format="fasta" name="single"
+              label="Reads without corresponding mate from datasets ${A.hid} and ${B.hid}"/>
+    </outputs>
 
- <help>
-**What it does**
- This tools joins paired end FASTA reads from separate files, one with the left mates and one with the right mates, into a single files.
- Last character in identifiers is used to distinguish pairs.
-  
-**Note !!!**
- This tools is to be used as more efficient replacement of FASTQ interlacer. Galaxy built-in FASTQ interlacer allows different ordering
- of sequences in both files but this flexibility comes with high memory requirements when large files are used. FASTA interlacer is simple but order of magnitude 
- faster tools which can be used on files where reads are in the same order.
- 
- 
-</help>
+    <help>
+        **What it does**
+        This tools joins paired end FASTA reads from separate files, one with the left
+        mates and one with the right mates, into a single files.
+        Last character in identifiers is used to distinguish pairs.
 
- 
+        **Note !!!**
+        This tools is to be used as more efficient replacement of FASTQ interlacer. Galaxy
+        built-in FASTQ interlacer allows different ordering
+        of sequences in both files but this flexibility comes with high memory
+        requirements when large files are used. FASTA interlacer is simple but order of
+        magnitude
+        faster tools which can be used on files where reads are in the same order.
+
+
+    </help>
 </tool>