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various fixes
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@bernt-matthias
bernt-matthias committed Feb 21, 2025
1 parent 998c7f3 commit 2fdcf76
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1 change: 0 additions & 1 deletion tools/allegro/.lint_skip
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78 changes: 45 additions & 33 deletions tools/allegro/allegro.xml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,5 @@
<tool id="allegro" name="Allegro" version="@TOOL_VERSIO@.1" profile="21.05">
<tool id="allegro" name="Allegro" version="@TOOL_VERSION@.1" profile="21.05">
<description>Linkage and Haplotype analysis</description>
<xrefs>
<xref type="bio.tools">allegro</xref>
</xrefs>
<macros>
<token name="@TOOL_VERSION@">2</token>
<xml name="macro_inputs" >
Expand All @@ -11,8 +8,11 @@
<param name="inp_map" value="map.21" />
</xml>
</macros>
<xrefs>
<xref type="bio.tools">allegro</xref>
</xrefs>
<requirements>
<requirement type="package" version="@TOOL_VERSIO@">allegro</requirement>
<requirement type="package" version="@TOOL_VERSION@">allegro</requirement>
</requirements>
<version_command><![CDATA[
allegro 2>&1 | head -1 | awk -F' ' '{print $2}'
Expand Down Expand Up @@ -68,7 +68,11 @@ PAIRWISEIBD $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_pa
#if $cond_sim.opt_sim.value == 'yes'
SIMULATE $cond_sim.extra_sim_dloc $cond_sim.extra_sim_npre $cond_sim.extra_sim_rep $cond_sim.extra_sim_err $cond_sim.extra_sim_yield $cond_sim.extra_sim_het
SIMULATE #slurp
#if $cond_sim.extra_sim_dloc != ""
dloc:$cond_sim.extra_sim_dloc #slurp
#end if
npre:$cond_sim.extra_sim_npre rep:$cond_sim.extra_sim_rep err:$cond_sim.extra_sim_err yield:$cond_sim.extra_sim_yield het:$cond_sim.extra_sim_het
#end if
MAXMEMORY 102400
Expand Down Expand Up @@ -143,7 +147,7 @@ UNINFORMATIVE
<param name="extra_linkage_par_pen" type="text" value="p0/p1/p2" label="Penetrance" />
</when>
</conditional>
<param name="extra_linkage_par_het" type="float" value="" label="HET Frequency (leave blank for dynamic)" />
<param name="extra_linkage_par_het" type="float" value="" optional="true" label="HET Frequency (leave blank for dynamic)" />
</when>
</conditional>

Expand Down Expand Up @@ -199,7 +203,7 @@ UNINFORMATIVE
</param>
<when value="no" />
<when value="yes" >
<param name="extra_sim_dloc" type="float" value="" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." />
<param name="extra_sim_dloc" type="float" value="" optional="true" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." />
<param name="extra_sim_npre" type="integer" value="1" label="Number of prefiles to generate" />
<param name="extra_sim_rep" type="integer" value="1" label="How many times to repeat family pattern" />
<param name="extra_sim_err" type="float" value="0" min="0" label="Error Rate" />
Expand All @@ -212,52 +216,60 @@ UNINFORMATIVE
</inputs>

<outputs>
<data name="out_ihaplo" format="allegro_haplo" label="${tool.name} on ${on_string}: Haplotypes" />
<data name="out_fparam" format="allegro_linkage" label="${tool.name} on ${on_string}: Linkage" />
<data name="out_ihaplo" format="allegro_ihaplo" label="${tool.name} on ${on_string}: Haplotypes" />
<data name="out_fparam" format="allegro_fparam" label="${tool.name} on ${on_string}: Linkage" />
<data name="out_founder" format="allegro_descent" label="${tool.name} on ${on_string}: Descent" />
<data name="out_linexp" format="txt" label="${tool.name} on ${on_string}: Linear Expression" />
<data name="out_combined_cross" format="txt" label="${tool.name} on ${on_string}: Combined Crossovers" />
</outputs>

<tests>
<test><!-- Default Haplotypes -->
<!-- Default Haplotypes -->
<test>
<expand macro="macro_inputs" />

<param name="extra_linkage_type" value="classical" />
<param name="extra_linkage_mptspt" value="mpt" />
<param name="opt_haplotypes" value="yes" />

<conditional name="cond_haplotypes">
<param name="opt_haplotypes" value="yes" />
</conditional>
<output name="out_ihaplo" >
<assert_contents>
<has_text_matching expression="1\s+206003\s+111\s+112(\s+[012])+" />
</assert_contents>
</output>
</test>
<test><!-- Linkage with custom steps-->
<!-- Linkage with custom steps-->
<test>
<expand macro="macro_inputs" />

<param name="extra_linkage_type" value="classical" />
<param name="extra_linkage_mptspt" value="mpt" />
<param name="extra_linkage_mptspt" value="mpt" />
<param name="extra_steps" value="3" />
<param name="extra_maxstep" value="30" />


<conditional name="cond_haplotypes">
<section name="section_linkage">
<param name="extra_linkage_mptspt" value="mpt" />
<conditional name="cond_linktype" >
<param name="extra_linkage_type" value="classical" />
</conditional>
<conditional name="cond_steps" >
<param name="extra_steps" value="3" />
</conditional>
</section>
</conditional>
<output name="out_fparam" >
<assert_contents>
<has_text_matching expression="1(\s+[-0-9.]+){2}\s+rs2822572" />
</assert_contents>
</output>
</test>
<test><!-- Single-point linear expression test with power weights -->
<!-- Single-point linear expression test with power weights -->
<test>
<expand macro="macro_inputs" />

<param name="extra_linkage_type" value="allele_sharing" />
<param name="extra_linkage_mptspt" value="spt" />
<param name="extra_linkage_linexp" value="lin" />
<param name="extra_linkage_scoring" value="homoz" />
<param name="extra_weighting" value="power:50" />

<conditional name="cond_haplotypes">
<section name="section_linkage">
<param name="extra_linkage_mptspt" value="spt" />
<conditional name="cond_linktype" >
<param name="extra_linkage_type" value="allele_sharing" />
<param name="extra_linkage_linexp" value="lin" />
<param name="extra_linkage_scoring" value="homoz" />
<param name="extra_weighting" value="power:0.5" />
</conditional>
</section>
</conditional>
<output name="out_fparam" >
<assert_contents>
<has_text_matching expression='(\-\d+\.\d+\s+)+rs2822696' />
Expand Down

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