<tool id="pbccs" name="CCS" version="0.1.0" python_template_version="3.5">
    <description>Generate accurate consensus sequences from subreads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"> <![CDATA[
    mkdir -p ./tmp &&
    cp '$input_file' ./tmp/input.bam &&
    cd ./tmp/ &&
    ccs
    -j 4
    #if $input_filter_options.minLength:
        --minLength '$input_filter_options.minLength'
    #end if
    #if $input_filter_options.maxLength:
        --maxLength '$input_filter_options.maxLength'
    #end if
    #if $input_filter_options.minPasses:
        --minPasses '$input_filter_options.minPasses'
    #end if
    #if $input_filter_options.minIdentity:
        --minIdentity '$input_filter_options.minIdentity'
    #end if
    #if $input_filter_options.zmws:
        --zmws '$input_filter_options.zmws'
    #end if
    #if $model_override_options.modelPath:
        --modelPath '$model_override_options.modelPath'
    #end if
    #if $model_override_options.modelSpec:
        --modelSpec '$model_override_options.modelSpec'
    #end if
    #if $output_filter_options.minPredictedAccuracy:
        --minPredictedAccuracy '$output_filter_options.minPredictedAccuracy'
    #end if
    #if $output_filter_options.minReadScore:
        --minReadScore '$output_filter_options.minReadScore'
    #end if
    #if $output_filter_options.maxDropFraction:
        --maxDropFraction  '$output_filter_options.maxDropFraction'
    #end if
    #if $processing_options.byStrand:
        --byStrand '$processing_options.byStrand'
    #end if
    #if $processing_options.noPolish:
	--noPolish '$processing_options.noPolish'
    #end if
    #if $processing_options.richQVs:
        --richQVs '$processing_options.richQVs'
    #end if 
    #if $if_log.log_options == "yes":
        --logFile  '$log_output'
        --logLevel '$if_log.loglevel'
    #end if
    #if $output_options.reportFile:
        --reportFile ccs_report.txt
    #end if
    input.bam
    output.bam 
    && mv output.bam '$bam_output'
    && mv ccs_report.txt '$report_output' 
    2>&1
    
    ]]></command>
    <inputs>
	<param name="input_file" type="data" format="bam" label="Input Subreads" help="Subreads (subreads.bam)"/>
	<section name="input_filter_options" title="Input Filter Options" expanded="False">
	       <param argument="--minLength" type="integer" value="10" label="Minimum length" help="Minimum draft length before polishing. [10]" />
	       <param argument="--maxLength" type="integer" value="21000"  label="Maximum length" help="Maximum draft length before polishing. [21000]"/>
	       <param argument="--minPasses" type="integer" value="3" label="Minimum number of subreads" help="Minimum number of subreads required to generate CCS. [3]" />
	       <param argument="--minIdentity" type="float" value="0.82" label="top N passes" help="Minimum identity of a subread aligned to the draft consensus to use it for polishing. 0 disables this filter. [0.82]" />
	       <param argument="--minSnr" type="float" value="2.5" label="Minimum SNR of subreads" help="Minimum SNR of subreads to use for generating CCS [2.5]"/>
	       <param argument="--zmws" type="text" value="all" label="Generate CCS for the provided comma-separated hole number ranges only." help="Default=all" />
       </section>
       <section name="model_override_options" title="Model Override Options" expanded="False">
	       <param argument="--modelPath" type="data" format="txt" optional="True" label="Model File" help="a model file or directory containing model files." />
               <param argument="--modelSpec" type="text" value="" optional="True"  label="Chemistry" help="Name of chemistry or model to use, overriding default selection."/>
       </section>
	<section name="processing_options" title="Processing Options" expanded="False">
	    <param argument="--byStrand" type="boolean" truevalue="--byStrand" falsevalue="" checked="false" label="Generate a consensus for each strand." />
	    <param argument="--noPolish" type="boolean" truevalue="--noPolish" falsevalue="" checked="false" label="Only output the initial template derived from the POA (faster, less accurate)." />
	    <param argument="--richQVs" type="boolean" truevalue="--richQVs" falsevalue="" checked="false" label="Emit dq, iq, and sq rich quality tracks." />
        </section>
	<section name="output_filter_options" title="Output Flter Options" expanded="False">
	       <param argument="--minPredictedAccuracy" type="float" value="0.9" label="Mininum predicted accurary" help="i.e 0.9"/>
               <param argument="--minReadScore" type="float" value="0.75"  label="Minimum read score of input subreads" help="i.e 0.75"/>
               <param argument="--maxDropFraction" type="float" value="0.34" label="Maximum fraction of subreads dropped by polishing (not input filters) before skipping ZMW." help="i.e 0.34" />
	</section>
	<section name="output_options" title="Output Files Options" expanded="False">
            <param argument="--reportFile" type="boolean" truevalue="True" falsevalue="False" checked="False" label="write the results report."/>
        </section>
	<conditional name="if_log">
		<param type="select" name="log_options" label="show log option">
		      <option value="yes">Yes</option>
		      <option value="no" selected="true">No</option> 
	        </param>
		<when value="yes">
                      <param argument="--logLevel" name="loglevel" type="select" label="Log Level">
                        <option selected="True" value="WARN">WARN</option>
                        <option value="TRACE">TRACE</option>
                        <option value="DEBUG">DEBUG</option>
                        <option value="INFO">INFO</option>
			<option value="FATAL">FATAL</option>
		      </param>
	        </when>
		<when value="no">
		</when>
        </conditional>
    </inputs>
    <outputs>
	    <data format="bam" name="bam_output" label="${tool.name} on ${on_string}: CCS reads in BAM format"/>
	    <data format="txt" name="report_output" label="${tool.name} on ${on_string}: CCS reads report"/>
	    <data format="txt" name="log_output" label="${tool.name} on ${on_string}: log" >
		  <filter>if_log['log_options'] == 'yes' </filter>
	    </data>
    </outputs>
    <tests>
        <test><!-- test with default settings -->
                 <param name="input_file" ftype="bam" value="input.subreads.bam"/>
                 <output name="bam_output" ftype="bam" file="output.bam" />
                 <output name="log_output" ftype="txt" file="log.txt" />
                 <output name="report_output" ftype="txt" file="report.txt" />
        </test>
    </tests>
    <help><![CDATA[
@PBCCS_OVERVIEW@

For detailed information on psp-gen, click here_, or view the license_.

.. _here: https://github.com/nlhepler/pbccs
.. _license: https://github.com/nlhepler/pbccs/blob/master/LICENSE

**Command Documentation**

CCS will generate consensus sequence.


    ]]></help>
    <expand macro="citations"/>
</tool>