Mercurial > repos > iuc > hal_halbranchmutations
diff hal_halBranchMutations.xml @ 0:a84e089a22f8 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 10:35:23 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hal_halBranchMutations.xml Fri Feb 06 10:35:23 2026 +0000 @@ -0,0 +1,156 @@ +<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> \ No newline at end of file