Mercurial > repos > p.lucas > taxid_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb

changeset 2:ad27c2b4e2c3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update: add txt format for input file
author p.lucas
date Thu, 28 Sep 2023 07:42:15 +0000
parents f83dad3524f9
children c6fc401b61b2
files TAXID_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb.xml
diffstat 1 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/TAXID_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb.xml	Thu Sep 21 15:23:24 2023 +0000
+++ b/TAXID_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb.xml	Thu Sep 28 07:42:15 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="TAXID_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb" name="Used after Get acc number for complete genome after MEGABLAST_TAB_select_acc_under_taxids" version="1.0">
+<tool id="TAXID_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb" name="Used after Get acc number for complete genome after MEGABLAST_TAB_select_acc_under_taxids" version="1.1">
   <description>
     From a file of taxid and accession numbers (tsv), deduce species taxids, get ref genome acc nr list (all chr).
     (it will allow to have complete genomes when aligning with host to remove host reads)
@@ -15,8 +15,8 @@
     python '$__tool_directory__/TAXID_genusexpand_taxid2acc_offline_searchinhostcompletegenomedb.py' -i ${input} -d ${taxid_host_db} -o ${output}
   ]]></command>
   <inputs>
-    <param name="input" format="tsv" type="data" label="Select tsv file with list of taxid and accession number." help="tsv output of MEGABLAST_TAB_select_acc_under_taxids.py (One taxid acc nbr per line)"/>
-    <param name="taxid_host_db" format="tsv" type="data" label="Select tsv file for HOSTS." help="taxid acc_number list in tsv (tabular separated at each line) for HOSTS"/>
+    <param name="input" format="tsv,txt" type="data" label="Select tsv file with list of taxid and accession number." help="tsv output of MEGABLAST_TAB_select_acc_under_taxids.py (One taxid acc nbr per line)"/>
+    <param name="taxid_host_db" format="tsv,txt" type="data" label="Select tsv file for HOSTS." help="taxid acc_number list in tsv (tabular separated at each line) for HOSTS"/>
   </inputs> 
   <outputs>
     <data name="output" format="txt" label="COMPLETE GENOME FROM ${tool.name} on ${on_string}"/>