Mercurial > repos > iuc > ena_webin_cli

diff process_input.py @ 1:93fac0ae859f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit abb15194a196267142d88b9348facf9e85e601ef
author iuc
date Mon, 06 Oct 2025 12:13:19 +0000
parents c9f87770ba8f
children
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line diff
--- a/process_input.py	Tue Aug 05 11:53:57 2025 +0000
+++ b/process_input.py	Mon Oct 06 12:13:19 2025 +0000
@@ -113,6 +113,12 @@
                         output_handle.write("STUDY\t" + study_accession + "\n")
                         output_handle.write("SAMPLE\t" + sample_accession + "\n")
                         output_handle.write("FASTA\t" + sample_alias + '.fasta.gz' + "\n")
+                        agp_path = os.path.join("./fasta", sample_alias + ".agp")
+                        if os.path.exists(agp_path):
+                            output_handle.write("AGP\t" + sample_alias + ".agp\n")
+                        chr_list_path = os.path.join("./fasta", sample_alias + ".tsv.gz")
+                        if os.path.exists(chr_list_path):
+                            output_handle.write("CHROMOSOME_LIST\t" + sample_alias + ".tsv.gz\n")
 
                     found_metadata = True
                     written_manifests_out.write(manifest_path + '\n')