diff data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml @ 0:c669787306ae draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml	Tue Feb 03 10:08:46 2015 -0500
@@ -0,0 +1,116 @@
+<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.1" tool_type="manage_data">
+    <description>fetching</description>
+    <command interpreter="python">data_manager_fetch_genome_all_fasta_dbkeys.py "${out_file}" 
+    #if str( $dbkey_source.dbkey_source_selector ) == 'existing':
+    --dbkey_description ${ dbkey_source.dbkey.get_display_text() }
+    #else
+    --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }"
+    #end if
+    
+    </command>
+    <inputs>
+        <conditional name="dbkey_source">
+          <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one.">
+            <option value="existing" selected="True">Existing</option>
+            <option value="new">New</option>
+          </param>
+          <when value="existing">
+              <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
+          </when>
+          <when value="new">
+              <param type="text" name="dbkey" value="" label="dbkey" optional="False" />
+              <param type="text" name="dbkey_name" value="" label="Display name for dbkey" />
+          </when>
+        </conditional>
+        
+        <param type="text" name="sequence_name" value="" label="Name 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="ucsc" selected="True">UCSC</option>
+            <option value="ncbi">NCBI</option>
+            <option value="url">URL</option>
+            <option value="history">History</option>
+            <option value="directory">Directory on Server</option>
+          </param>
+          <when value="ucsc">
+            <param type="text" name="requested_dbkey" value="" label="UCSC's DBKEY for source FASTA" optional="False" />
+          </when>
+          <when value="ncbi">
+            <param type="text" name="requested_identifier" value="" label="NCBI identifier" optional="False" />
+          </when>
+          <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" 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 original data instead of copying" checked="False" />
+          </when>
+        </conditional>
+        <conditional name="sorting">
+          <param name="sort_selector" type="select" label="Choose the source for the reference genome">
+            <option value="as_is" selected="True">As is</option>
+            <option value="lexicographical">Lexicographical</option>
+            <option value="gatk">GATK</option>
+            <option value="custom">Custom</option>
+          </param>
+          <when value="as_is">
+          </when>
+          <when value="lexicographical">
+          </when>
+          <when value="gatk">
+          </when>
+          <when value="custom">
+            <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1">
+                <param type="text" name="identifier" value="" label="Sequence Identifier" optional="False" />
+            </repeat>
+            <conditional name="handle_not_listed">
+                <param name="handle_not_listed_selector" type="select" label="How to handle non-specified Identifiers">
+                    <option value="discard" selected="True">Discard</option>
+                    <option value="keep_append">Keep and Append</option>
+                    <option value="keep_prepend">Keep and Prepend</option>
+                </param>
+                <when value="discard">
+                </when>
+                <when value="keep_append">
+                </when>
+                <when value="keep_prepend">
+                </when>
+            </conditional>
+          </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 reference genome from various sources (UCSC, NCBI, URL, Galaxy History, or a server directory) and populates the "all_fasta" data table.
+
+------
+
+
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
+
+    </help>
+</tool>