diff pyCrac_galaxy/makeFasta.xml @ 0:ae088f9b2f2e draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyCrac_galaxy/makeFasta.xml	Thu Jun 06 09:39:32 2013 -0400
@@ -0,0 +1,79 @@
+<tool id="makeFasta" name="Extract IDs" force_history_refresh="True">
+	  <description>from Read Aligner output</description>
+ 	  <command interpreter="perl">
+	#if $format.formatChoice == "fasta" #makeFasta.pl --input $input --genes "$genes.g" --outFormat $format.formatChoice --out $out --id $out.id  --output_path $__new_file_path__ 
+	#else #makeFasta.pl --input $input --genes "$genes.g" --outFormat $format.formatChoice --limit $format.limit --out $out --id $out.id  --output_path $__new_file_path__ 
+	#end if#
+	
+ 	  </command>
+ 	  <inputs>
+	      <param name="input" type="data" format="fasta" label="Read Aligner output file" help="Fasta file"/>
+		<conditional name="genes">
+		<param name="choice" type="select" label="Choose IDs by">
+           				 <option value="index">ID Index File</option>
+           				 <option value="number" selected="true">Text Box</option>
+       		</param>
+		<when value="index">
+			<param name="indices" type="data" format="tabular" label="ID Index"/>
+	      		<param name="g" type="select" multiple="true" accept_default="true" label="ID" >
+		 		<options from_dataset="indices">
+		 			<column name="name" index="0"/>
+		 			<column name="value" index="0"/>
+		 		</options>
+	      		</param>
+		</when> 
+		<when value="number">		
+	      		<param name="g" type="text" format="txt" size="200" value="" label="IDs" help="Enter identifiers separated by a comma">
+				<validator type="empty_field" />
+			</param>
+		</when>
+		</conditional>	
+		<conditional name="format">
+		<param name="formatChoice" type="select" label="Choose output format">
+           				 <option value="fasta" selected="true">Fasta</option>
+           				 <option value="align">Tabular Alignment</option>
+           				 <option value="both">Both</option>
+       		</param>
+		<when value="align">
+			<param name="limit" type="integer" format="integer" value="90" size="4" label="Set the column width of alignment" help="Enter a value > 50">
+				<validator type="in_range" min="50" message="Please enter a value greater than 50"/>
+	       		</param>
+		</when> 
+		<when value="both">
+			<param name="limit" type="integer" format="integer" value="90" size="4" label="Set the column width of alignment" help="Enter a value > 50">
+				<validator type="in_range" min="50" message="Please enter a value greater than 50"/>
+	       		</param>
+		</when> 
+		<when value="fasta">		
+		</when>
+		</conditional>
+ 	  </inputs>
+ 	  <outputs>
+	    <data name="out" format="txt" label="Extract IDs"/>
+ 	  </outputs>
+	  <help>
+.. class:: infomark
+
+**What it does**
+
+Splits the fasta pyReadAligner output in to individual files per selected ID.
+
+To select IDs by text box
+
+	- Enter identifiers separated by a comma e.g RDN37-1,RPL7A,SNR17A.
+
+To select IDs by ID index file
+
+	- Provide a file of data type indexfile (use pencil icon to edit data type)
+	- The index file should contain all possible IDs in the first column
+	- Select multiple IDs by holding Shift or Ctrl keys
+
+Output formats
+
+	- Fasta - Output reads and reference sequence in fasta format
+	- Alignment tab - Format output to show read sequences aligned to reference sequence
+	- Both - Output both of the formats above
+
+ 	  </help>
+</tool>
+