Mercurial > repos > iuc > hal_hal2vg
diff hal_hal2vg.xml @ 0:cb1771706300 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac
| author | iuc |
|---|---|
| date | Fri, 06 Feb 2026 10:37:20 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hal_hal2vg.xml Fri Feb 06 10:37:20 2026 +0000 @@ -0,0 +1,122 @@ +<tool id="hal_hal2vg" name="hal2vg" version="1.1.8+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>converts HAL to a vg-compatible sequence graph</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="1.1.8">hal2vg</requirement> + </requirements> + <expand macro="stdio"/> + <command detect_errors="aggressive"><![CDATA[ + hal2vg + #if $rootGenome: + --rootGenome '$rootGenome' + #end if + #if $mode.reference == '--refGenomes': + --refGenomes '$mode.refGenomes' + #end if + #if $selection.filter == '--targetGenomes': + --targetGenomes '$selection.targetGenomes' + #else if $selection.filter == '--ignoreGenomes': + --ignoreGenomes '$selection.ignoreGenomes' + #end if + #if $outputFormat == 'hg': + --outputFormat 'hg' + #end if + --chop $chop + $noAncestors + '$input_hal' > '$output_file' + ]]></command> + <inputs> + <expand macro="input_hal"/> + <conditional name="mode"> + <param name="reference" type="select" label="Genomes to treat as reference paths" help="Specify genomes to treat as reference paths with all others as haplotype paths"> + <option value="" selected="true">All genomes (default)</option> + <option value="--refGenomes">Specific reference genomes (--refGenomes)</option> + </param> + <when value=""/> + <when value="--refGenomes"> + <param name="refGenomes" type="text" value="" label="List of genomes" help="Enter a comma-separated (no spaces) list of genomes to use as reference genomes"> + <expand macro="sanitizer_default"/> + <expand macro="validator_comma_list"/> + </param> + </when> + </conditional> + <expand macro="params_rootGenome_optional"/> + <conditional name="selection"> + <param name="filter" type="select" label="Genome selection filters"> + <option value="" selected="true">All genomes (default)</option> + <option value="--targetGenomes">Specific genomes to target (--targetGenomes)</option> + <option value="--ignoreGenomes">Specific genomes to ignore (--ignoreGenomes)</option> + </param> + <when value=""/> + <when value="--targetGenomes"> + <expand macro="params_targetGenomes"/> + </when> + <when value="--ignoreGenomes"> + <param name="ignoreGenomes" type="text" value="" label="List of genome" help="Comma-separated (no spaces) list of genomes to ignore"> + <expand macro="sanitizer_default"/> + <expand macro="validator_comma_list"/> + </param> + </when> + </conditional> + <param argument="--noAncestors" type="boolean" truevalue="--noAncestors" falsevalue="" checked="false" label="No ancestors" help="Don't write ancestral paths, nor sequence exclusive to ancestral genomes"/> + <param argument="--chop" type="integer" min="0" value="0" label="Chop" help="Chop up nodes in output graph so they are not longer than given length"/> + <param name="outputFormat" type="select" label="Output format"> + <option value="pg" selected="true">pg (default)</option> + <option value="hg">hg</option> + </param> + </inputs> + <outputs> + <data name="output_file" format="hal.pg" label="${tool.name} on ${on_string}: Graph"> + <change_format> + <when input="outputFormat" value="hg" format="hal.hg"/> + </change_format> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <output name="output_file" ftype="hal.pg" file="hal2vg_output.pg"/> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <param name="outputFormat" value="hg"/> + <output name="output_file" ftype="hal.hg" file="hal2vg_output.hg"/> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <param name="rootGenome" value="Genome_0"/> + <conditional name="mode"> + <param name="reference" value="--refGenomes"/> + <param name="refGenomes" value="Genome_0,Genome_1"/> + </conditional> + <output name="output_file" ftype="hal.pg" file="hal2vg_refGenomes_output.pg"/> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <param name="noAncestors" value="true"/> + <output name="output_file" ftype="hal.pg" file="hal2vg_noAncestors_output.pg"/> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="selection"> + <param name="filter" value="--targetGenomes"/> + <param name="targetGenomes" value="Genome_0,Genome_1"/> + </conditional> + <param name="chop" value="10"/> + <output name="output_file" ftype="hal.pg" file="hal2vg_targetGenomes_chop_output.pg"/> + </test> + </tests> + <help><![CDATA[ +hal2vg converts a HAL file to a vg-compatible sequence graph. +The tool generates a graph representation where genomes can be treated as reference paths or haplotypes, optionally excluding ancestral sequences or selected genomes. +Control node length via chopping, select target or reference genomes, and choose the output format (PG or HG). + +Use it for constructing genome graphs for downstream analyses such as variant calling, pangenome visualization, or graph-based mapping. + ]]></help> + <citations> + <citation type="doi">10.1038/s41587-023-01793-w</citation> + </citations> + <expand macro="creator"/> +</tool> \ No newline at end of file