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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 10:35:23 +0000 |
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<tool id="hal_halbranchmutations" name="halBranchMutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>identifies mutations on a branch between given genome and its parent</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command detect_errors="aggressive"><![CDATA[ halBranchMutations #if $support.file == 'true': --refTargets '$support.refTargets' #end if #if $mode.export == 'sequence': --refSequence '$mode.sequence' #end if --start $start --length $length --maxGap $maxGap --maxNFraction $maxNFraction --refFile stdout --snpFile stdout --delBreakFile stdout --parentFile '$output_parentFile' '$input_hal' '$refGenome' > '$output_file' ]]></command> <inputs> <expand macro="input_hal"/> <param name="refGenome" type="text" value="" label="Reference genome" help="To be analyzed branch and its according parent. Must denote bottom node in a branch, and therefore cannot be the root itself"> <expand macro="sanitizer_default"/> <expand macro="validator_trim"/> </param> <conditional name="support"> <param name="file" type="select" label="Use a BED file for coordinates" help="Use a BED file to define intervals in the reference genome to process"> <option value="false" selected="true">No, don't use a BED file (default)</option> <option value="true">Yes, use a BED file (--refTargets)</option> </param> <when value="false"/> <when value="true"> <param name="refTargets" type="data" format="bed" label="BED file"/> </when> </conditional> <conditional name="mode"> <param name="export" type="select" label="Sequence process options"> <option value="default" selected="true">Process all sequences (default)</option> <option value="sequence">Process a reference sequence (--refSequence)</option> </param> <when value="default"/> <when value="sequence"> <expand macro="params_sequence"/> </when> </conditional> <expand macro="params_start"/> <expand macro="params_length"/> <expand macro="params_maxGap"/> <expand macro="params_maxNFraction"/> </inputs> <outputs> <data name="output_file" format="bed" label="${tool.name} on ${on_string}"/> <data name="output_parentFile" format="bed" label="${tool.name} on ${on_string}: Rearrangements in reference's parent genome"/> </outputs> <tests> <test expect_num_outputs="2"> <param name="input_hal" value="halTest.hal"/> <param name="refGenome" value="Genome_1"/> <output name="output_file" ftype="bed"> <assert_contents> <has_line line="#Sequence	Start	End	MutationID	ParentGenome	ChildGenome"/> <has_line line="Genome_1_seq	1465	1758	I	Genome_0	Genome_1"/> <has_line line="Genome_1_seq	4395	4688	P	Genome_0	Genome_1"/> <has_n_lines n="5"/> </assert_contents> </output> <output name="output_parentFile" ftype="bed"> <assert_contents> <has_line line="#Sequence	Start	End	MutationID	ParentGenome	ChildGenome"/> <has_line line="Genome_0_seq	293	879	U	Genome_0	Genome_1"/> <has_line line="Genome_0_seq	586	879	U	Genome_0	Genome_1"/> <has_n_lines n="13"/> </assert_contents> </output> </test> <test expect_num_outputs="2"> <param name="input_hal" value="halTest.hal"/> <param name="refGenome" value="Genome_1"/> <param name="start" value="10"/> <param name="length" value="500"/> <output name="output_file" ftype="bed"> <assert_contents> <has_line line="#Sequence	Start	End	MutationID	ParentGenome	ChildGenome"/> <has_n_lines n="2"/> </assert_contents> </output> <output name="output_parentFile" ftype="bed"> <assert_contents> <has_line line="#Sequence	Start	End	MutationID	ParentGenome	ChildGenome"/> <has_line line="Genome_0_seq	293	879	U	Genome_0	Genome_1"/> <has_n_lines n="3"/> </assert_contents> </output> </test> <test expect_num_outputs="2"> <param name="input_hal" value="halTest.hal"/> <param name="refGenome" value="Genome_1"/> <conditional name="mode"> <param name="export" value="sequence"/> <param name="sequence" value="Genome_1_seq"/> </conditional> <output name="output_file" ftype="bed"> <assert_contents> <has_line line="#Sequence	Start	End	MutationID	ParentGenome	ChildGenome"/> <has_line line="Genome_1_seq	1465	1758	I	Genome_0	Genome_1"/> <has_line line="Genome_1_seq	4395	4688	P	Genome_0	Genome_1"/> <has_n_lines n="5"/> </assert_contents> </output> <output name="output_parentFile" ftype="bed"> <assert_contents> <has_line line="#Sequence	Start	End	MutationID	ParentGenome	ChildGenome"/> <has_line line="Genome_0_seq	293	879	U	Genome_0	Genome_1"/> <has_line line="Genome_0_seq	586	879	U	Genome_0	Genome_1"/> <has_n_lines n="13"/> </assert_contents> </output> </test> <test expect_num_outputs="2"> <param name="input_hal" value="halTest.hal"/> <param name="refGenome" value="Genome_1"/> <conditional name="support"> <param name="file" value="true"/> <param name="refTargets" value="halBranchMutations.bed"/> </conditional> <output name="output_file" ftype="bed"> <assert_contents> <has_line line="#Sequence	Start	End	MutationID	ParentGenome	ChildGenome"/> <has_line line="Genome_1_seq	1465	1758	I	Genome_0	Genome_1"/> <has_line line="Genome_1_seq	4395	4688	P	Genome_0	Genome_1"/> <has_n_lines n="5"/> </assert_contents> </output> <output name="output_parentFile" ftype="bed"> <assert_contents> <has_line line="#Sequence	Start	End	MutationID	ParentGenome	ChildGenome"/> <has_line line="Genome_0_seq	586	879	U	Genome_0	Genome_1"/> <has_line line="Genome_0_seq	1172	1465	U	Genome_0	Genome_1"/> <has_n_lines n="13"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ halBranchMutations detects mutations that occurred on the branch between a chosen genome and its parent in a HAL alignment. It reports point mutations, deletions, duplications, and other structural changes in an output BED file. ]]></help> <expand macro="citation"/> <expand macro="creator"/> </tool>