diff sra_macros.xml @ 13:c38286ea7047 draft

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

--- a/sra_macros.xml	Wed Sep 26 05:33:56 2018 -0400
+++ b/sra_macros.xml	Wed Oct 17 11:44:12 2018 -0400
@@ -1,10 +1,34 @@
 <macros>
     <token name="@VERSION@">2.9.1</token>
+    <token name="@ACCESSIONS_FROM_FILE@">
+        grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
+    </token>
+    <token name="@SET_ACCESSIONS@"><![CDATA[
+        #if $input.input_select=="file_list":
+            for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ;
+            do (
+        #elif $input.input_select=="accession_number":
+            acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
+        #end if
+    ]]></token>
+
     <macro name="requirements">
         <requirements>
             <requirement type="package" version="2.9.1">sra-tools</requirement>
         </requirements>
     </macro>
+    <macro name="sanitize_query">
+        <sanitizer>
+            <valid initial="string.printable">
+                <remove value=" "/>
+                <remove value="&apos;" />
+            </valid>
+            <mapping initial="none">
+                <add source=" " target=""/>
+                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
+            </mapping>
+        </sanitizer>
+    </macro>
     <macro name="input_conditional">
         <conditional name="input">
             <param name="input_select" type="select" label="select input type">
@@ -14,14 +38,7 @@
             </param>
             <when value="accession_number">
                 <param name="accession" type="text" label="Accession" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809">
-                    <sanitizer>
-                        <valid initial="string.printable">
-                            <remove value=" "/>
-                        </valid>
-                        <mapping initial="none">
-                            <add source=" " target=""/>
-                        </mapping>
-                    </sanitizer>
+                    <expand macro="sanitize_query" />
                     <validator type="empty_field" message="An accession is required"/>
                 </param>
             </when>