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

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<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>