diff sra_pileup.xml @ 13:c38286ea7047 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91

--- a/sra_pileup.xml	Wed Sep 26 05:33:56 2018 -0400
+++ b/sra_pileup.xml	Wed Oct 17 11:44:12 2018 -0400
@@ -9,7 +9,7 @@
         <![CDATA[
 
         #if $input.input_select=="accession_number":
-            acc="${input.accession}" &&
+            acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] &&
         #end if
 
         ## Need to set the home directory to the current working directory,
@@ -38,7 +38,7 @@
         #elif $input.input_select == "accession_number":
             "\$acc" > "$output_accession"
         #elif $input.input_select == "text":
-            `cat "$input.text"` > "$output_text"
+            `@ACCESSIONS_FROM_FILE@ '$input.text'` > "$output_text"
         #end if
         ]]>
     </command>
@@ -54,14 +54,7 @@
             </when>
             <when value="accession_number">
                 <param format="text" name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743">
-                    <sanitizer>
-                        <valid initial="string.printable">
-                            <remove value=" "/>
-                        </valid>
-                        <mapping initial="none">
-                            <add source=" " target=""/>
-                        </mapping>
-                    </sanitizer>
+                    <expand macro="sanitize_query" />
                 </param>
             </when>
             <when value="text">