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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac
| author | iuc |
|---|---|
| date | Fri, 06 Feb 2026 10:38:29 +0000 |
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<tool id="hal_hal2maf" name="hal2maf" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>converts HAL to MAF</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command detect_errors="aggressive"><![CDATA[ #if $file.append == 'true': ## If an input MAF file is provided to append to, ensure that it is not modified. cp '$input_maf' writable_maf.maf && #end if hal2maf #if $file.append == 'true': --append #end if #if $genome.reference == 'custom': --refGenome '$genome.refGenome' $genome.noAncestors #end if #if $filter.option == '--targetGenomes': --targetGenomes '$filter.targetGenomes' #else if $filter.option == '--rootGenome': --rootGenome '$filter.rootGenome' #end if #if $convert.mode == 'sequence': --refSequence '$convert.sequence' --start $convert.start --length $convert.length #else if $convert.mode == 'target': --refTargets '$convert.refTargets' #else if $convert.mode == 'global': --global #end if --maxRefGap $maxRefGap --maxBlockLen $maxBlockLen $noDupes $onlySequenceNames $unique $printTree $onlyOrthologs $keepEmptyRefBlocks '$input_hal' writable_maf.maf #if $compression.type == 'gz': && gzip -c writable_maf.maf > '$output_file' #else if $compression.type == 'bz2': && bzip2 -c writable_maf.maf > '$output_file' #else: && mv writable_maf.maf '$output_file' #end if ]]></command> <inputs> <expand macro="input_hal"/> <expand macro="params_conditional_refGenome"/> <conditional name="filter"> <param name="option" type="select" label="Genomes to include in the output"> <option value="" selected="true">All genomes (default)</option> <option value="--targetGenomes">Specific target genomes (--targetGenomes)</option> <option value="--rootGenome">Only genomes in the subtree to a root (--rootGenome)</option> </param> <when value=""/> <when value="--targetGenomes"> <expand macro="params_targetGenomes"/> </when> <when value="--rootGenome"> <expand macro="params_rootGenome"/> </when> </conditional> <conditional name="convert"> <param name="mode" type="select" label="Convert options"> <option value="" selected="true">All sequences (default)</option> <option value="sequence">A reference sequence (--refSequence)</option> <option value="target">Using reference intervals from a BED file (--refTargets)</option> <option value="global">All columns in alignment, ignoring reference-based filters (--global)</option> </param> <when value=""/> <when value="sequence"> <expand macro="params_sequence"/> <expand macro="params_start"/> <expand macro="params_length"/> </when> <when value="target"> <param name="refTargets" type="data" format="bed" label="BED file" help="BED file with reference genome intervals to convert. Only alignment columns overlapping these intervals are included"/> </when> <when value="global"/> </conditional> <conditional name="file"> <param name="append" type="select" label="Append new alignment to an existing MAF file"> <option value="false" selected="true">No, create a new MAF file (default)</option> <option value="true">Yes, append to an existing MAF file (--append)</option> </param> <when value="true"> <param name="input_maf" type="data" format="maf" label="MAF file"/> </when> <when value="false"/> </conditional> <param argument="--maxRefGap" type="integer" min="0" value="0" label="Maximum gap length" help="Maximum gap length in reference genome"/> <param argument="--maxBlockLen" type="integer" min="0" value="1000" label="Maximum block length" help="Maximum length of MAF block in output"/> <param argument="--noDupes" type="boolean" truevalue="--noDupes" falsevalue="" checked="false" label="Ignore paralogy edges" help="Ignore paralogy edges"/> <expand macro="params_onlySequenceNames"/> <param argument="--unique" type="boolean" truevalue="--unique" falsevalue="" checked="false" label="Unique" help="Only write column whose left-most reference coordinate is in the specified range. This is used to ensure that the same column isn't sampled twice (due to duplications) by MAFs generated on distinct ranges"/> <param argument="--printTree" type="boolean" truevalue="--printTree" falsevalue="" checked="false" label="Print Tree" help="Print a gene tree for every block"/> <param argument="--onlyOrthologs" type="boolean" truevalue="--onlyOrthologs" falsevalue="" checked="false" label="Only Orthologs" help="Make only orthologs to the reference appear in the MAF blocks"/> <param argument="--keepEmptyRefBlocks" type="boolean" truevalue="--global" falsevalue="" checked="false" label="Keep empty reference blocks" help="Keep blocks that contain no reference sequence"/> <expand macro="params_conditional_compression"/> </inputs> <outputs> <data name="output_file" format="maf" label="${tool.name} on ${on_string}: MAF file"> <change_format> <when input="compression.type" value="gz" format="maf.gz"/> <when input="compression.type" value="bz2" format="maf.bz2"/> </change_format> </data> </outputs> <tests> <test expect_num_outputs="1"> <param name="input_hal" value="halTest.hal"/> <conditional name="filter"> <param name="option" value=""/> </conditional> <output name="output_file" ftype="maf"> <assert_contents> <has_line line="##maf version=1 scoring=N/A"/> <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/> <has_line line="a"/> <has_text text="s	Genome_0.Genome_0_seq	293	293	+	1758"/> <has_text text="s	Genome_1.Genome_1_seq	4571	117	+	5472"/> <has_n_lines n="90"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="input_hal" value="halTest.hal"/> <conditional name="filter"> <param name="option" value=""/> </conditional> <conditional name="compression"> <param name="type" value="gz"/> </conditional> <output name="output_file" ftype="maf.gz" file="hal2maf_output.maf.gz"/> </test> <test expect_num_outputs="1"> <param name="input_hal" value="halTest.hal"/> <conditional name="filter"> <param name="option" value=""/> </conditional> <conditional name="compression"> <param name="type" value="bz2"/> </conditional> <output name="output_file" ftype="maf.bz2" file="hal2maf_output.maf.bz2"/> </test> <test expect_num_outputs="1"> <param name="input_hal" value="halTest.hal"/> <conditional name="filter"> <param name="option" value="--rootGenome"/> <param name="rootGenome" value="Genome_1"/> </conditional> <param name="printTree" value="true"/> <param name="onlySequenceNames" value="true"/> <output name="output_file" ftype="maf"> <assert_contents> <has_line line="##maf version=1 scoring=N/A"/> <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/> <has_text text="a tree="/> <has_text text="Genome_1_seq,Genome_1_seq,Genome_2,Genome_3,Genome_3)Genome_0_seq;"/> <has_text text="Genome_0_seq	293	293	+	1758"/> <has_text text="s	Genome_1_seq	4864	117	+	5472"/> <has_n_lines n="52"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="input_hal" value="halTest.hal"/> <param name="maxBlockLen" value="200"/> <param name="noDupes" value="true"/> <output name="output_file" ftype="maf"> <assert_contents> <has_line line="##maf version=1 scoring=N/A"/> <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/> <has_line line="a"/> <has_text text="s	Genome_3.Genome_3_seq	4102	200	+	6139"/> <has_text text="s	Genome_1.Genome_1_seq	3130	93	+	5472"/> <has_text text="s	Genome_0.Genome_0_seq	1748	10	+	1758	CGCGTCGGCG"/> <has_n_lines n="69"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="input_hal" value="halTest.hal"/> <conditional name="genome"> <param name="reference" value="custom"/> <param name="refGenome" value="Genome_1"/> <param name="noAncestors" value="true"/> </conditional> <param name="onlyOrthologs" value="true"/> <output name="output_file" ftype="maf"> <assert_contents> <has_line line="##maf version=1 scoring=N/A"/> <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/> <has_line line="a"/> <has_text text="s	Genome_1.Genome_1_seq	5135	337	+	5472"/> <has_text text="s	Genome_2.Genome_2_seq	2498	139	+	4270"/> <has_text text="s	Genome_3.Genome_3_seq	4571	117	+	6139"/> <has_n_lines n="230"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="input_hal" value="halTest.hal"/> <conditional name="genome"> <param name="reference" value="custom"/> <param name="refGenome" value="Genome_1"/> </conditional> <param name="unique" value="true"/> <output name="output_file" ftype="maf"> <assert_contents> <has_line line="##maf version=1 scoring=N/A"/> <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/> <has_line line="a"/> <has_text text="s	Genome_3.Genome_3_seq	1033	139	+	6139"/> <has_text text="s	Genome_0.Genome_0_seq	1348	117	+	1758"/> <has_text text="s	Genome_1.Genome_1_seq	5274	198	+	5472	NNNNNNNNNNNNNNNN"/> <has_n_lines n="96"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="input_hal" value="halTest.hal"/> <conditional name="genome"> <param name="reference" value="custom"/> <param name="refGenome" value="Genome_1"/> </conditional> <param name="maxRefGap" value="2000"/> <output name="output_file" ftype="maf"> <assert_contents> <has_line line="##maf version=1 scoring=N/A"/> <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/> <has_line line="a"/> <has_text text="s	Genome_2.Genome_2_seq	2344	154	+	4270"/> <has_text text="s	Genome_1.Genome_1_seq	1465	293	+	5472	----------------"/> <has_text text="s	Genome_1.Genome_1_seq	3516	293	+	5472	NNNNNNNNNNNNNNNN"/> <has_n_lines n="101"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="input_hal" value="halTest.hal"/> <conditional name="convert"> <param name="mode" value="sequence"/> <param name="sequence" value="Genome_0_seq"/> <param name="start" value="4"/> <param name="length" value="10"/> </conditional> <output name="output_file" ftype="maf"> <assert_contents> <has_line line="##maf version=1 scoring=N/A"/> <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/> <has_line line="a"/> <has_line line="s	Genome_0.Genome_0_seq	4	10	+	1758	TCGGGGGGGA"/> <has_line line="s	Genome_2.Genome_2_seq	4	10	+	4270	TCGGGGGGGA"/> <has_line line="s	Genome_3.Genome_3_seq	4	10	+	6139	TCGGGGGGGA"/> <has_n_lines n="11"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="input_hal" value="halTest.hal"/> <conditional name="file"> <param name="append" value="true"/> <param name="input_maf" value="hal2maf_append.maf"/> </conditional> <conditional name="filter"> <param name="option" value="--targetGenomes"/> <param name="targetGenomes" value="Genome_2,Genome_3"/> </conditional> <output name="output_file" ftype="maf"> <assert_contents> <has_line line="##maf version=1 scoring=N/A"/> <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/> <has_line line="a"/> <has_text text="s	Genome_1.Genome_1_seq	0	293	+	5472"/> <has_text text="s	Genome_3.Genome_3_seq	4395	176	+	6139"/> <has_text text="s	Genome_1.Genome_1_seq	3223	176	+	5472"/> <has_n_lines n="152"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="input_hal" value="halTest.hal"/> <conditional name="convert"> <param name="mode" value="global"/> </conditional> <output name="output_file" ftype="maf"> <assert_contents> <has_line line="##maf version=1 scoring=N/A"/> <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/> <has_line line="a"/> <has_text text="s	Genome_1.Genome_1_seq	3516	293	+	5472	NNNNNNNNNNNN"/> <has_text text="s	Genome_2.Genome_2_seq	1465	293	+	4270	------------"/> <has_text text="s	Genome_3.Genome_3_seq	4571	117	+	6139"/> <has_n_lines n="113"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="input_hal" value="halTest.hal"/> <conditional name="convert"> <param name="mode" value="target"/> <param name="refTargets" value="hal2maf.bed"/> </conditional> <output name="output_file" ftype="maf"> <assert_contents> <has_line line="##maf version=1 scoring=N/A"/> <has_line line="# hal (Genome_1:1,Genome_2:1,Genome_3:1)Genome_0;"/> <has_line line="a"/> <has_text text="s	Genome_0.Genome_0_seq	0	293	+	1758"/> <has_text text="s	Genome_2.Genome_2_seq	3516	293	+	4270"/> <has_text text="s	Genome_3.Genome_3_seq	586	293	+	6139"/> <has_n_lines n="24"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ hal2maf converts an input HAL alignment into a MAF file as output. The tool supports converting the full alignment or restricting output to a selected reference genome, reference sequence, a set of target genomes, or only genomes belonging to the subtree rooted at a root genome. Additional controls allow filtering for orthologs, excluding ancestral sequences, keeping empty reference blocks, limiting block size, and controlling reference gaps. MAF blocks can also include gene tree annotations if requested. ]]></help> <expand macro="citation"/> <expand macro="creator"/> </tool>