Mercurial > repos > dfornika > blast_report_basic

changeset 6:b8a3578b6445 draft

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Uploaded
author dfornika
date Tue, 03 Mar 2020 05:33:55 +0000
parents c7ce2cd96546
children 445a1923bb97
files blast_report_basic.xml
diffstat 1 files changed, 4 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/blast_report_basic.xml	Tue Mar 03 01:16:59 2020 +0000
+++ b/blast_report_basic.xml	Tue Mar 03 05:33:55 2020 +0000
@@ -3,9 +3,10 @@
     <command>
         <![CDATA[
           python '${__tool_directory__}/blast_report.py' 
-            -f ${filter_pident}:$filter_kws
+            --min-identity ${min_identity}
+	    --filter-keywords '${filter_kws}'
             #if str($bins) != "None"
-              -b "${bins}"
+              -b '${bins}'
             #end if
             $discard_redundant
 	    '${tabular_blast_report_input}'
@@ -16,7 +17,7 @@
     </command>
     <inputs>
         <param name="tabular_blast_report_input" type="data" format="tabular" label="Tabular BLAST results (extended 26 columns)"/>
-        <param name="filter_pident" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/>
+        <param name="min_identity" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/>
         <param name="filter_kws" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/>
         <param name="bins" type="select" label="Database bins" multiple="true" display="checkboxes">
             <options from_data_table="blast_reference_bins">