Mercurial > repos > iuc > allegro
changeset 1:ef4a081bc97b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/ commit bb83e01055cde8c766c630bec27afd3402ad6c88
| author | iuc |
|---|---|
| date | Fri, 21 Feb 2025 21:22:41 +0000 |
| parents | 8c29e3621475 |
| children | |
| files | allegro.xml |
| diffstat | 1 files changed, 48 insertions(+), 33 deletions(-) [+] |
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--- a/allegro.xml Sat Dec 09 06:39:42 2017 -0500 +++ b/allegro.xml Fri Feb 21 21:22:41 2025 +0000 @@ -1,15 +1,18 @@ -<tool id="allegro" name="Allegro" version="@VER@.0" > +<tool id="allegro" name="Allegro" version="@TOOL_VERSION@.1" profile="21.05"> <description>Linkage and Haplotype analysis</description> <macros> - <token name="@VER@">2</token> + <token name="@TOOL_VERSION@">2</token> <xml name="macro_inputs" > <param name="inp_ped" value="pedin.21" /> <param name="inp_dat" value="datain.21" /> <param name="inp_map" value="map.21" /> </xml> </macros> + <xrefs> + <xref type="bio.tools">allegro</xref> + </xrefs> <requirements> - <requirement type="package" version="@VER@">allegro</requirement> + <requirement type="package" version="@TOOL_VERSION@">allegro</requirement> </requirements> <version_command><![CDATA[ allegro 2>&1 | head -1 | awk -F' ' '{print $2}' @@ -32,7 +35,7 @@ #end if #elif $cond_haplotypes.opt_haplotypes.value == 'no' #if $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'defaults' -MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par ${opt_xlinked} het param.mpt ${out_fparam} +MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value par $opt_xlinked het param.mpt ${out_fparam} #elif $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_type.value == 'allele_sharing' MODEL $cond_haplotypes.section_linkage.extra_linkage_mptspt.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_linexp.value $cond_haplotypes.section_linkage.cond_linktype.extra_linkage_scoring.value $cond_haplotypes.section_linkage.cond_linktype.extra_weighting.value param.mpt ${out_linexp} @@ -52,7 +55,7 @@ #end if #end if -#if $opt_xlinked.value == 'X' +#if $opt_sexspecific SEXSPECIFIC on #end if @@ -65,7 +68,11 @@ #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:$cond_sim.extra_sim_het #end if MAXMEMORY 102400 @@ -140,7 +147,7 @@ <param name="extra_linkage_par_pen" type="text" value="p0/p1/p2" label="Penetrance" /> </when> </conditional> - <param name="extra_linkage_par_het" type="float" value="" label="HET Frequency (leave blank for dynamic)" /> + <param name="extra_linkage_par_het" type="float" value="" optional="true" label="HET Frequency (leave blank for dynamic)" /> </when> </conditional> @@ -196,7 +203,7 @@ </param> <when value="no" /> <when value="yes" > - <param name="extra_sim_dloc" type="float" value="" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." /> + <param name="extra_sim_dloc" type="float" value="" optional="true" min="0" label="Disease Locus (cM). Leave blank for unlinked disease locus." /> <param name="extra_sim_npre" type="integer" value="1" label="Number of prefiles to generate" /> <param name="extra_sim_rep" type="integer" value="1" label="How many times to repeat family pattern" /> <param name="extra_sim_err" type="float" value="0" min="0" label="Error Rate" /> @@ -209,52 +216,60 @@ </inputs> <outputs> - <data name="out_ihaplo" format="allegro_haplo" label="${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' />