--- a/macros.xml	Fri Jun 23 21:31:47 2023 +0000
+++ b/macros.xml	Mon Aug 26 14:59:07 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.0.5</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@TOOL_VERSION@">3.1.1</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="edam_ontology">
         <edam_topics>
@@ -15,8 +15,8 @@
     <macro name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">sra-tools</requirement>
-            <requirement type="package" version="2.6">pigz</requirement>
-            <requirement type="package" version="1.17">samtools</requirement>
+            <requirement type="package" version="2.8">pigz</requirement>
+            <requirement type="package" version="1.20">samtools</requirement>
             <yield/>
         </requirements>
     </macro>
@@ -36,11 +36,6 @@
     <token name="@COPY_CONFIGFILE@"><![CDATA[
         mkdir -p ~/.ncbi &&
         cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg &&
-        vdb-config -s "/repository/user/main/public/root=\$PWD" &&
-        vdb-config -s "/repository/user/ad/public/root=\$PWD" &&
-        vdb-config -s "/repository/user/default-path=\$PWD" &&
-        vdb-config -s "/repository/user/main/public/root=\$PWD" &&
-        vdb-config -s /http/timeout/read=10000 &&
     ]]></token>
     <token name="@SET_ACCESSIONS@"><![CDATA[
         #if $input.input_select == "sra_file":
@@ -69,6 +64,11 @@
 /config/default = "false"
 /libs/temp_cache = "."
 /tools/prefetch/download_to_cache = "false"
+/http/timeout/read = "1000"
+/repository/user/main/public/root = "."
+/repository/user/ad/public/root = "."
+/repository/user/default-path = "."
+/repository/user/main/public/root = "."
             ]]></configfile>
         </configfiles>
     </macro>
@@ -116,13 +116,42 @@
         <param name="minMapq" type="integer" min="0" max="42" label="Minimum mapping quality" optional="true" help="Minimum mapping quality an alignment has to have, to be dumped." argument="--min-mapq"/>
     </macro>
     <macro name="region">
-        <param format="text" name="region" type="text" label="aligned region" optional="true"
+        <param name="region" type="text" label="aligned region" optional="true"
                help="Filter by position on genome. Can be either accession.version (ex: NC_000001.10), chromosome name (ex:chr1 or 1) or 1-based coordinates (ex: chr1:1-101)." argument="--aligned-region"/>
     </macro>
     <macro name="matepairDist">
         <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
                help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference" argument="--matepair-distance"/>
     </macro>
+    <macro name="defline" tokens="defline_param,defline_default">
+        <param argument="@DEFLINE_PARAM@" value="@DEFLINE_DEFAULT@" type="text" label="Defline format specification for sequence">
+            <help>A string of characters and/or variables. The variables can be one of:
+                $ac: accession, $si: spot id, $sn: spot name, $sg: spot group (barcode), $sl: spot length in bases, $ri: read number, $rn: read name, $rl: read length in bases.
+                '[]' could be used for an optional output: if all vars in [] yield empty values whole group is not printed. Empty value is empty string or for numeric variables.
+                Ex: @$sn[_$rn]/$ri '_$rn' is omitted if name is empty"</help>
+            <!-- allow many chars, but quotes and backslash -->
+            <sanitizer>
+                <valid initial="string.ascii_letters,string.digits">
+                    <add value="@" />
+                    <add value="$" />
+                    <add value="[" />
+                    <add value="]" />
+                    <add value="_" />
+                    <add value="-" />
+                    <add value="+" />
+                    <add value="." />
+                    <add value=";" />
+                    <add value=":" />
+                    <add value="/" />
+                    <add value="?" />
+                    <add value=" " />
+                    <add value="=" />
+                </valid>
+            </sanitizer>
+            <validator type="regex" message="Must start with @">^.*</validator>
+
+        </param> 
+    </macro>
     <macro name="citation">
         <citations>
             <citation type="doi">10.1093/nar/gkq1019</citation>