diff TrustStoreGalaxyImport.xml @ 5:159d2159e745

Add list files.

--- a/TrustStoreGalaxyImport.xml	Thu Dec 12 13:07:45 2013 +1100
+++ b/TrustStoreGalaxyImport.xml	Thu Dec 12 16:17:43 2013 +1100
@@ -9,6 +9,7 @@
     <command interpreter="python">TrustStoreGalaxyImport.py https://tstest-kms.it.csiro.au/kmscolab_3_0 https://tstest-ims.it.csiro.au/ims_3_0/services/IMS $username $password desktop cpU92F1PT7VOCANjSknuCDp4DrubmujoBaF6b0miz8OpKNokEbGMHCaSFK5/lISbBmaaGVCgeADI2A39F3Hkeg== $storename $path $filename $output</command>
     <inputs>
         <param name="file_type" type="select" label="File Format" help="Which format is the data you're downloading?">
+            <option value="just list files"/>
             <option value="ab1"/>
             <option value="axt"/>
             <option value="bam"/>
@@ -42,7 +43,7 @@
         </param>
         <!-- <param name="kms_url" type="text" label="kms url" help="the remote url for your key management service" value="http://localhost:8080/TSSKeyManagementService-Collaboration" size="200" />
         <param name="ims_url" type="text" label="ims url" help="the remote url for your integrity management service" value="http://localhost:8080/TSSIntegrityManagementService/services/IMS" size="200" /> -->
-        <param name="username" type="text" label="username" help="kms username" value="user" size="20" >
+        <param name="username" type="text" label="Username" help="Your KMS username, e.g. [e-mail]" value="user" size="20" >
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
@@ -52,7 +53,7 @@
                 </mapping>
             </sanitizer>
         </param>
-        <param name="password" type="text" label="password" help="kms password" value="password" size="1">
+        <param name="password" type="text" label="Password" help="Your KMS password" value="password" size="1">
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
@@ -65,11 +66,11 @@
         <!-- <param name="client_key" type="text" label="client key" help="kms client name" value="my-trusted-client-with-secret" size="20" /> -->
         <!-- <param name="client_secret" type="text" label="client secret" help="kms client secret" value="somesecret" size="20" /> -->
         <param name="storename" type="text" label="Store Name" help="e.g.: My Galaxy Store" value="galaxy" size="20" />
-        <param name="path" type="text" label="Path in store" help="e.g.: /rawdata/feb2014/, leave as / for top level files" value="/" size="20" />
-        <param name="filename" type="text" label="File name" help="e.g.: export1.bam" value="1.png" size="20" />
+        <param name="path" type="text" label="Path in Store" help="e.g.: /rawdata/feb2014/, leave as / for top level files" value="/" size="20" />
+        <param name="filename" type="text" label="Filename" help="e.g.: export1.bam. Leave empty if 'just list files' is chosen above." value="" size="20" />
     </inputs>
     <outputs>
-        <data name="output" format="ab1">
+        <data name="output" format="txt">
             <change_format>
                 <when input="file_type" value="ab1" format="ab1" />
                 <when input="file_type" value="axt" format="axt" />
@@ -101,6 +102,7 @@
                 <when input="file_type" value="txt" format="txt" />
                 <when input="file_type" value="wig" format="wig" />
                 <when input="file_type" value="xml" format="xml" />
+                <when input="file_type" value="just list files" format="txt"/>
             </change_format>
         </data>
     </outputs>