changeset 1:259d3e864091 draft default tip

Uploaded

--- a/data_manager/directory_data_manager.xml	Wed Mar 23 04:03:26 2016 -0400
+++ b/data_manager/directory_data_manager.xml	Wed Mar 23 07:28:11 2016 -0400
@@ -2,10 +2,6 @@
     <description>path inputer</description>
     <command interpreter="python">
         directory_data_manager.py
-        --value "${value}" 
-        --dbkey "${dbkey}" 
-        --name "${name}" 
-        --path "${path}" 
         --data_table_name "directory_data" 
         --json_output_file "${json_output_file}"
     </command>
@@ -28,25 +24,56 @@
     <help>
 Adds information for downloading data to the directory_data data table.
 
-Reguried inputs are.
+Reguried inputs
+===============
+
+path
+----
+
+Full path on the server where galaxy can find the files
+
+Original Extension
+------------------
 
-path: Full path on the server where galaxy can find the files
+The Extention as found on the server.
+
+Parts before the extension that could be used to split the data into seubsection such are Read1 and Read2 should not e included.
 
-Original Extension: The Extention as found on the server.
-    Parts before the extension that could be used to split the data into seubsection such are Read1 and Read2 should not e included.
+Galaxy_Extension
+----------------
+
+The Extention to give the file before loading into galaxy so galaxy can detect the file type.
+
+This should be one as listed in galaxy/config/datatypes_conf.xml (or xml.sample)
+
+For example use tabular for tsv, txt for text and fasta and not fa\n
 
-Galaxy_Extension: The Extention to give the file before loading into galaxy so galaxy can detect the file type.
-    This should be one as listed in galaxy/config/datatypes_conf.xml (or xml.sample)
-    For example use tabular for tsv, txt for text and fasta and not fa
-    Ideally use fastqsanger, fastqsolexa, fastqcssanger, or fastqillumina instead of just fastq as many tools need this level of detail.
+Ideally use fastqsanger, fastqsolexa, fastqcssanger, or fastqillumina instead of just fastq as many tools need this level of detail.
+
+Decompress
+----------
+
+'Yes' to ask the tool to decompress the files otherwise 'No'.
+
+Any other value will cause an error. 
+
+Optional Inputs
+===============
 
-Decompress: 'Yes' to ask the tool to decompress the files otherwise 'No'. Any other value will cause an error. 
+Name
+----
 
-If name is not provided the filename from path less the exstension is used.
+If not provided the last bit of **path**  is used.
 
-If value is not provided, the name will be used (or its default)
+Value
+-----
+
+If value is not provided, the **name** will be used (or its default)
 
-If dbkey is not provided, the value will be used (or its default)
+dbkey
+-----
+
+If not provided, the **value** will be used (or its default)
 
 ===
 

--- a/tool_data_table_conf.xml.sample	Wed Mar 23 04:03:26 2016 -0400
+++ b/tool_data_table_conf.xml.sample	Wed Mar 23 07:28:11 2016 -0400
@@ -1,7 +1,6 @@
-<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
 <tables>
     <table name="directory_data" comment_char="#">
         <columns>value, dbkey, name, original_extension, galaxy_extension, decompress, path</columns>
         <file path="tool-data/directory_data.loc" />
     </table>
- </tables>
+</tables>