diff data_manager/data_manager_fetch_tx2gene.xml @ 0:a4d4da89aae1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_tx2gene.xml	Wed Oct 10 05:44:36 2018 -0400
@@ -0,0 +1,68 @@
+<tool id="data_manager_fetch_gff" name="Create entries in tx2gene data table" version="0.0.1" tool_type="manage_data">
+    <description>fetching</description>
+    <command><![CDATA[
+       python "$__tool_directory__"/data_manager_fetch_tx2gene.py "${out_file}"
+       --type $file_type
+       --dbkey_description ${ dbkey.get_display_text() }
+       --base_dir $__tool_directory__
+        
+    ]]></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_id" value="" label="ID for sequence" />
+ 
+        <param name="file_type" type="select" label="Select input type: GFF/GTF file(features will be extracted to create tx2gene table) or transcript to gene table file(tab separated)">
+                <option value="gff_gtf">GFF/GTF file</option>
+                <option value="tx2gene">tx2gene</option>
+            </param>
+	<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" />
+	    </when>
+	    <when value="history">
+		<param name="input_fasta" type="data" label="File from History" multiple="False" optional="False" />
+	    </when>
+	    <when value="directory">
+		<param type="text" name="filename" value="" label="Full path to File on disk" optional="False" />
+		<param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" />
+	    </when>
+	</conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <!-- TODO: need some way to test that new entry was added to data table -->
+        <test>
+            <param name="dbkey" value="anoGam1"/>
+            <param name="sequence_name" value=""/>
+            <param name="sequence_desc" value=""/>
+            <param name="sequence_id" value=""/>
+            <param name="reference_source_selector" value="history"/>
+            <param name="input_fasta" value="phiX174.fasta"/>
+            <param name="sort_selector" value="as_is"/>
+            <output name="out_file" file="phiX174.data_manager_json"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Fetches a gff file from various sources (URL, Galaxy History, or a server directory) and populates the "all_gff" data table.
+
+------
+
+
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+
+    </help>
+</tool>