# HG changeset patch
# User mvdbeek
# Date 1429103317 14400
# Node ID cb2d94bb67727fdbed52aeeaabbcf7b25c6b0289
# Parent  3dcce035dd6c7d3aeba78bf22826d35eee9778a6
Uploaded

diff -r 3dcce035dd6c -r cb2d94bb6772 generate_sliding_windows.xml
--- a/generate_sliding_windows.xml	Wed Apr 15 07:57:55 2015 -0400
+++ b/generate_sliding_windows.xml	Wed Apr 15 09:08:37 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="generate_sliding_windows" name="generate_sliding_windows"  version="0.1.2">
+<tool id="generate_sliding_windows" name="generate_sliding_windows"  version="0.1.3">
 <description>Split fasta sequence in nucleotide windows</description>
     <requirements>
         <requirement type="package" version="1.65">biopython</requirement>
@@ -11,7 +11,21 @@
         generate_sliding_windows.py --input "$input" --output "$output" --window $window --step $step
     ]]></command>
     <inputs>
-        <param type="data" name="input" label="input fasta file" help="select fasta file for which you wish to generate a multi-fasta file in a sliding window fashion" format="fasta" />
+        <conditional name="refFastaSource">
+            <param help="" label="Will you select a fasta sequence from your history or use a pre-installed sequence?" name="fastaSource" type="select">
+                <option value="history">Use one from the history</option>
+                <option value="pre-installed">Use a pre-installed fasta sequence</option>
+            </param>
+            <when value="pre-installed">
+                <param help="if you wish to have your fasta sequence listed contact instance administrator" label="Select a fasta sequence" name="input" type="select">
+                    <options from_data_table="all_fasta">
+          </options>
+                </param>
+            </when>
+            <when value="history">
+                <param format="fasta" label="Select a fasta file for which you wish to generate a multi-fasta file in a sliding window fashion" name="input" type="data" />
+            </when>
+        </conditional>
         <param type="integer" name="window" value="21" min="1" label="window size" help="Specifiy the size of the windows that should be generated"/>
         <param type="integer" name="step" value="21" min="1" label="step size" help="Specify the distance with which windows should be spaced apart."/>
     </inputs>
diff -r 3dcce035dd6c -r cb2d94bb6772 tool-data/all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Wed Apr 15 09:08:37 2015 -0400
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 3dcce035dd6c -r cb2d94bb6772 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Apr 15 09:08:37 2015 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>