<tool id="filterinfo" name="Report proportion of reads in one file vs. the other" version="0.1.0">
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
	'$__tool_directory__/filterinfo.sh' -1 
#if str( $orig_cond.orig_type ) == "one_of_pair"
	'$orig_cond.orig'
#else
	'$orig_cond.orig.forward'
#end if
	-2
#if str( $filtered_cond.filtered_type ) == "one_of_pair"
	'$filtered_cond.filt'
#else
	'$filtered_cond.filt.forward'
#end if
#if $ispaired
	'-p'
#end if
	-o '$out'
    ]]></command>
    <inputs>
	    <conditional name="orig_cond">
		<param name="orig_type" type="select" label="Original Input Type">
		    <option value="one_of_pair">Fastq File</option>
                    <option value="paired_collection">Paired Collection</option>
		</param>
		<when value="one_of_pair">
                    <param name="orig" type="data" format="fastqsanger" label="Fastq sequences before filtering" help="Specify a single fastq file (either unpaired or half of a pair)"/>
		</when>
		<when value="paired_collection">
		    <param name="orig" format="fastqsanger" type="data_collection" collection_type="paired" label="Fastq sequences before filtering" help="Specify paired dataset collection containing paired reads"/>
		</when>
            </conditional>
	    <conditional name="filtered_cond">
		<param name="filtered_type" type="select" label="Filtered Input Type">
		    <option value="one_of_pair">Fastq File</option>
                    <option value="paired_collection">Paired Collection</option>
		</param>
		<when value="one_of_pair">
                    <param name="filt" type="data" format="fastqsanger" label="Fastq sequences before filtering" help="Specify a single fastq file (either unpaired or half of a pair)"/>
		</when>
		<when value="paired_collection">
		    <param name="filt" format="fastqsanger" type="data_collection" collection_type="paired" label="Fastq sequences before filtering" help="Specify paired dataset collection containing paired reads"/>
		</when>
            </conditional>
            <param name="ispaired" type="boolean" label="Do the input fastq files come from sets of paired reads?"/>
    </inputs>
    <outputs>
	    <data name="out" format="tabular" />
    </outputs>
    <tests>
	    <test>
		    <param name="orig_type" value="paired_collection"/>
		    <param name="orig">
			<collection type="paired">
			    <element name="forward" value="full.fq" />
			    <element name="reverse" value="full2.fq" />
			</collection>
		    </param>
		    <param name="filtered_type" value="one_of_pair"/>
		    <param name="filt" value="filtered.fq"/>
                    <param name="ispaired" value="true"/>
		    <output name="out" file="prop.tsv"/>
	    </test>
    </tests>
    <help><![CDATA[
	Usage: ./filterinfo.sh -1 full.fq -2 filtered.fq -o out.tsv

]]></help>
    <citations>
	     <citation type="bibtex">
@misc{githubfilterinfo,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {filterinfo},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/jashay90/galaxytools},
}</citation>
    </citations>
</tool>