changeset 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>

--- a/fastq_dump.xml	Fri Jun 23 21:32:08 2023 +0000
+++ b/fastq_dump.xml	Mon Sep 11 08:37:23 2023 +0000
@@ -22,7 +22,7 @@
         fastq-dump --accession "\$acc"
         --split-files
     #end if
-    --defline-seq '@\$sn[_\$rn]/\$ri'
+    --defline-seq '$adv.defline_seq'
     --defline-qual '+'
 
     $adv.split
@@ -91,6 +91,7 @@
             <option value="fastqsanger.bz2">bzip2 compressed fastq</option>
         </param>
         <section name="adv" title="Advanced Options" expanded="False">
+            <expand macro="defline" defline_param="--defline-seq" defline_default="@$sn[_$rn]/$ri"/>
             <param name="minID" type="integer" label="Minimum spot ID" optional="true" help="Minimum spot id to be dumped." argument="--minSpotId"/>
             <param name="maxID" type="integer" label="Maximum spot ID" optional="true" help="Maximum spot id to be dumped." argument="--maxSpotId"/>
             <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="--minReadLen"/>

--- a/macros.xml	Fri Jun 23 21:32:08 2023 +0000
+++ b/macros.xml	Mon Sep 11 08:37:23 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.0.5</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="edam_ontology">
         <edam_topics>
@@ -123,6 +123,33 @@
         <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="?" />
+                </valid>
+            </sanitizer>
+            <validator type="regex" message="Must start with @">^.*</validator>
+
+        </param> 
+    </macro>
     <macro name="citation">
         <citations>
             <citation type="doi">10.1093/nar/gkq1019</citation>