diff sra_macros.xml @ 1:462ee06c9358 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede

--- a/sra_macros.xml	Sun Dec 06 09:04:37 2015 -0500
+++ b/sra_macros.xml	Tue May 17 14:14:50 2016 -0400
@@ -1,9 +1,10 @@
 <macros>
     <macro name="requirements">
         <requirements>
-            <requirement type="package" version="1.1.3">ngs_sdk</requirement>
-            <requirement type="package" version="2.5.2">ncbi_vdb</requirement>
-            <requirement type="package" version="2.5.2">sra_toolkit</requirement>
+            <requirement type="package" version="1.2.3">ngs_sdk</requirement>
+            <requirement type="package" version="2.6.2">ncbi_vdb</requirement>
+            <requirement type="package" version="2.6.2">sra_toolkit</requirement>
+            <requirement type="package" version="2.6.2">sra-tools</requirement>
             <requirement type="package" version="5.18.1">perl</requirement>
         </requirements>
     </macro>
@@ -12,13 +13,17 @@
             <param name="input_select" type="select" label="select input type">
                 <option value="accession_number">SRR accession</option>
                 <option value="file">SRA archive in current history</option>
+                <option value="file_list">List of SRA accession, one per line</option>
             </param>
             <when value="accession_number">
-                <param name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743"/>
+                <param name="accession" type="text" label="SRR accession" help="Must start with SRR,DRR or ERR, e.g. SRR925743 , ERR343809"/>
             </when>
             <when value="file">
                 <param format="sra" name="file" type="data" label="sra archive"/>
             </when>
+            <when value="file_list">
+                <param format="txt" name="file_list" type="data" label="sra accession list"/>
+            </when>            
         </conditional>
     </macro>
     <macro name="alignments">
@@ -45,8 +50,16 @@
             <citation type="doi">10.1093/nar/gkq1019</citation>
         </citations>
     </macro>
-    <token name="@SRATOOLS_ATTRRIBUTION@">Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
+    <token name="@SRATOOLS_ATTRRIBUTION@">
+        Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
+        
         Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
+
+        Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ). 
+        
         Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
-        For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.</token>
+        
+        For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.
+        
+    </token>
 </macros>