primertool.xml

<tool id="primertool" name="PrimerTool" version="0.1.0">
    <description>Generate primer order list from plasmids.</description>
    <command detect_errors="exit_code"><![CDATA[
      docker run -v $__tool_directory__:/tools -v /export/galaxy-central/database/files:/export/galaxy-central/database/files:rw -v /export/galaxy-central/database/job_working_directory:/export/galaxy-central/database/job_working_directory:rw -v $__tool_directory__/data:/data -v $__tool_data_path__:/tmp  -e SBC_ASSEMBLY_PATH=/tools/code/sbc-assembly -e DATA=/data -e ICE_SERVER=$ice.input2 -e ICE_USERNAME=$ice.input3 -e ICE_PASSWORD=$ice.input4 -e ICE_GROUP=$ice.input6 sbc1 python /tools/primerTool.py -enzymes $input1 -temp $input2 -iceServer $ice.input2 -iceUser $ice.input3 -icePass $ice.input4
	#if $input_type == 'true':
	   -plate $input3 
	#end if 
	-plasmids $input4 -output $output1 -tempFolder $output1.extra_files_path
    ]]></command>
    <inputs>
    	<param name="input1" type="text" label="Restriction enzymes" value="MlyI"
	       help="Comma separated restriction enzymes" />
    	<param name="input2" type="float" label="Melting temperature" value="60" help="Melting temperature" />
	<conditional name="input_type">
	  <param name="input_type_selector" type="boolean" label="Input existing plate file" />
	  <when value="true">
    	    <param name="input3" type="data" label="Existing plate file" help="Existing plate file" format="csv"/>
	  </when>
	</conditional>
    	<param name="input4" type="data" label="Plasmids" help="Plasmid csv file" format="csv"/>
	    <section name="ice" title="ICE Options" expanded="false">
	      <param name="input2" type="text" label="ICE Server" help="ICE registry server"
		     value="https://ice.synbiochem.co.uk"/>
	      <param name="input3" type="text" label="ICE User" help="ICE user name">
		<sanitizer invalid_char="">
		  <valid initial="string.ascii_letters,string.digits,string.punctuation">
		    <add value="_" />
		  </valid>
		</sanitizer>
	      </param>
	      <param name="input4" type="text" label="ICE Pass" help="ICE login"/>
	      <sanitizer invalid_char="">
		<valid initial="string.ascii_letters,string.digits,string.punctuation">
		  <add value="_" />
		</valid>
	      </sanitizer>
	      <param name="input6" type="text" label="ICE Group" help="ICE Group" value="synbiochem"/>
	   </section>

    </inputs>
    <outputs>
        <data name="output1" format="csv" from_work_dir="out.csv" label="Primers for ${input4.name}"/>
    </outputs>
    <help><![CDATA[
    Primer tool: generates primer list from the list of plasmids in input files.
    
    - Inputs:
        - Restriction enzymes: comma separated restriction enzymes (MlyI, etc.).
        - Melting temperature.
        - Plate files (optional): *csv* files with plate primer information.
	- Plasmids: *csv* file with the list of plasmid ids.


    - Outputs:
        - *csv* file with the list of primers.
    
.. class:: infomark

Pablo Carbonell, SYNBIOCHEM, University of Manchester, 2020.


    ]]></help>
</tool>