# HG changeset patch
# User brenninc
# Date 1458732491 14400
# Node ID 259d3e8640919275251a1ceff3e56bf6288de5a2
# Parent d98ec2e7d5691df6f2a9813fdda1f9cba92089e8
Uploaded
diff -r d98ec2e7d569 -r 259d3e864091 data_manager/directory_data_manager.xml
--- 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 @@
path inputer
directory_data_manager.py
- --value "${value}"
- --dbkey "${dbkey}"
- --name "${name}"
- --path "${path}"
--data_table_name "directory_data"
--json_output_file "${json_output_file}"
@@ -28,25 +24,56 @@
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)
===
diff -r d98ec2e7d569 -r 259d3e864091 tool_data_table_conf.xml.sample
--- 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 @@
-
value, dbkey, name, original_extension, galaxy_extension, decompress, path
-
+