diff fasterq_dump.xml @ 30:4317d3cb6cba draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787

--- a/fasterq_dump.xml	Fri Jun 23 21:32:08 2023 +0000
+++ b/fasterq_dump.xml	Mon Sep 11 08:37:23 2023 +0000
@@ -14,7 +14,7 @@
     @SET_ACCESSIONS@
     while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
         fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
-        --seq-defline '@\$sn/\$ri'
+        --seq-defline '$adv.seq_defline'
         --qual-defline '+'
         $adv.split
         #if str( $adv.minlen ) != "":
@@ -71,6 +71,7 @@
     <inputs>
         <expand macro="input_conditional"/>
         <section name="adv" title="Advanced Options" expanded="False">
+            <expand macro="defline" defline_param="--seq-defline" defline_default="@$sn/$ri"/>
             <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--min-read-len"/>
             <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end).">
                 <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option>