lca.xml

<tool id="lca" name="lowest common ancestor">
<!-- <description>Find lowest common ancestor</description>-->
<requirements>
        <requirement type="package" version="3.8.2">python</requirement> 
    </requirements>
<command>
<![CDATA[
bash '$__tool_directory__/lca.sh'
$input
$output
$bitscore
$identity
$coverage
$setting_mode.setting
#if $setting_mode.setting == "best_hit" or $setting_mode.setting == "best_hits_range"
	$setting_mode.tophitid
	$setting_mode.tophitcoverage
#else
	"none"
	"none"
#end if
#if $filterhits
	$filterhits
#else
	"none"
#end if
#if $filterlcahits
	$filterlcahits
#else
	"none"
#end if
$minbitscore
#if $filtersource
    $filtersource
#else:
	"none"
#end if
]]>
</command>
	<macros>
	<macro name="best_hit_params">
		<param name="tophitid" type="float" label="Identity threshold" value="100" min="1" max="100"/>
		<param name="tophitcoverage" type="float" label="Query coverage threshold"  value="100" min="1" max="100"/>
	</macro>
	</macros>
<inputs>
<param format="tabular" name="input" type="data" label="BLAST output file"/>
<param name="bitscore" type="float" label="Top bitscore percentage cutoff"  value="8" min="1" max="100"/>
<param name="minbitscore" type="integer" label="Minimum bitscore"  value="100" min="1" max="1000"/>
<param name="identity" type="float" label="Minimum identity"  value="80" min="1" max="100"/>
<param name="coverage" type="float" label="Minimum coverage"  value="70" min="1" max="100"/>
	<conditional name="setting_mode">
					<param name="setting" type="select" multiple="false" label="Settings mode">
						<option value="best_hit" selected="true">Output the top hit as species identification if it is above the chosen threshold</option>
                        <option value="best_hits_range">Output all top hits above threshold</option>
						<option value="only_lca">Check lca on all hits</option>
					</param>
					<when value="best_hit">
						<expand macro="best_hit_params"/>
					</when>
                    <when value="best_hits_range">
						<expand macro="best_hit_params"/>
					</when>
				</conditional>
	<param name="filterhits" type="text" label="Don't use hits containing this taxonomy:" help="Comma separated"  value="environmental"/>
    <param name="filterlcahits" type="text" label="Ignore rank when containing:" help="Comma separated" value="unknown"/>
	<param name="filtersource" type="select" multiple="true" label="Don't use hits with taxonomy from:">
            <option value="BOLD" label="BOLD">BOLD</option>
            <option value="private_BOLD">private_BOLD</option>
            <option value="Genbank">Genbank</option>
        </param>
</inputs>


<outputs>
	<data format="tabular" name="output" label="$input.display_name lca" />
</outputs>
<tests>
<test>
<param name="test_input" value="test_input.txt"/>
<output name="test_output" file="test_output.txt"/>
</test>
</tests>
<help>
Find lca from blast output
</help>
</tool>