diff data_manager/novoalign_index_builder.xml @ 2:e51fb8188ed9 draft

planemo upload for repository https://github.com/zipho/data_manager_novoalign_index_builder commit 7c74dfc33ffac5de44aae81def9c374f5f5e2a20

--- a/data_manager/novoalign_index_builder.xml	Thu Mar 03 06:28:09 2016 -0500
+++ b/data_manager/novoalign_index_builder.xml	Thu Mar 03 08:40:42 2016 -0500
@@ -1,22 +1,22 @@
 <?xml version="1.0" encoding="utf-8" ?>
 <tool id="novoalign_index_builder" name="NOVO ALIGN index" tool_type="manage_data" version="0.0.1">
     <description>Build an index for use by the Novo Align mapping tool</description>
-    <requirements>
-        <requirement type="package" version="0.0.1d">novoalign</requirement>
-    </requirements>
     <stdio>
         <exit_code range=":-1" />
         <exit_code range="1:" />
     </stdio>
     <command interpreter="python">
-        novoalign_index_builder.py "${out_file}" --data_table_name "novo_index"
+        novoalign_index_builder.py "${out_file}" --dbkey_description ${ dbkey.get_display_text() } --data_table_name "novocraft_index"
     </command>
     <inputs>
+        <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
+        <param type="text" name="sequence_name" value="" label="Name of sequence" />
+        <param type="text" name="sequence_desc" value="" label="Description of sequence" />
+        <param type="text" name="sequence_id" value="" label="ID for sequence" />
         <conditional name="reference_source">
           <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
             <option value="url">URL</option>
             <option value="history">History</option>
-            <option value="directory">Directory on Server</option>
           </param>
           <when value="url">
             <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
@@ -24,10 +24,6 @@
           <when value="history">
             <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" />
           </when>
-          <when value="directory">
-            <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" />
-            <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" />
-          </when>
         </conditional>
     </inputs>
     <outputs>