changeset 2:000dbfafe31d draft default tip

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ef336d64317cbf496202203c7adcd368249e99f9

--- a/filter_assembly.xml	Mon Feb 03 14:37:31 2025 +0000
+++ b/filter_assembly.xml	Mon Jun 30 12:23:02 2025 +0000
@@ -1,7 +1,7 @@
-<tool name="Filter assemblies" id="filter_assemblies" version="2.0.4">
+<tool name="Filter assemblies" id="filter_assemblies" version="2.0.5">
 
     <description>
-        Filter the outputs of Velvet or Trinity assemblies
+        Filter the outputs of Spades, Velvet or Trinity assemblies
     </description>
 
     <macros>
@@ -34,7 +34,7 @@
 
     <inputs>
         <param name="inputs" type="data" format="fasta" multiple="true" label="Input files" />
-        <param name="percent_identity" type="integer" value="100" label="Overlap percent identity cutoff" help="Cap3 parameter (-p N); minimum percent identity of an overlap. The specified value should be more than 65%." />
+        <param name="percent_identity" type="integer" value="90" label="Overlap percent identity cutoff" help="Cap3 parameter (-p N); minimum percent identity of an overlap. The specified value should be more than 65%." />
         <param name="overlap_length" type="integer" value="60" label="Overlap length cutoff" help="Cap3 parameter (-o N); minimum length of an overlap (in base pairs). The specified value should be more than 15 base pairs." />
         <param name="length_seq_max" type="integer" value="100" label="Minimum sequence length" help="Keep sequences which length is higher than the minimum sequence length  " />
     </inputs>

--- a/scripts/S01_script_to_choose.py	Mon Feb 03 14:37:31 2025 +0000
+++ b/scripts/S01_script_to_choose.py	Mon Jun 30 12:23:02 2025 +0000
@@ -5,7 +5,6 @@
 
 from Bio import SeqIO
 
-
 def fasta_formatter(input_file, output_file):
     """
     Reformats the input FASTA file to ensure that sequences
@@ -27,7 +26,6 @@
         if sequence:
             outfile.write(sequence + '\n')
 
-
 def reformat_headers(input_file, output_file, prefix):
     """
     Reformats the headers of the FASTA records by adding a specified prefix
@@ -78,7 +76,6 @@
     # Write output file with new headers
     SeqIO.write(modified_sequences, output_fasta, "fasta")
 
-
 def main():
     if len(sys.argv) < 5:
         print(
@@ -152,6 +149,12 @@
         name_final_file = os.path.join(output_dir, tmp)
         fasta_formatter(name_fasta_final, name_final_file)
 
+        # Deletion of temporary files
+        os.remove(name_fasta_formatter)
+        os.remove(merged_file)
+        os.remove(cap_singlets_file)
+        os.remove(cap_contigs_file)
+        os.remove(name_fasta_final)
 
 if __name__ == "__main__":
     main()