Mercurial > repos > iuc > hal_halalignmentdepth
diff hal_halAlignmentDepth.xml @ 0:25489f7c4cff 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 10:35:39 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hal_halAlignmentDepth.xml Fri Feb 06 10:35:39 2026 +0000 @@ -0,0 +1,148 @@ +<tool id="hal_halalignmentdepth" name="halAlignmentDepth" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>makes a alignment depth wiggle plot for a genome</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command detect_errors="aggressive"><![CDATA[ + halAlignmentDepth + #if $genome.reference == 'custom': + $genome.noAncestors + #end if + #if $mode.export == 'sequence': + --refSequence '$mode.sequence' + #end if + --start $start + --length $length + ## --step $step ## Has a known bug https://github.com/ComparativeGenomicsToolkit/hal/issues/326 + #if $filter.option == '--targetGenomes': + --targetGenomes '$filter.targetGenomes' + #else if $filter.option == '--rootGenome': + --rootGenome '$filter.rootGenome' + #end if + $countDupes + '$input_hal' + #if $genome.reference == 'custom': + '$genome.refGenome' + #else + "\"\"" ## Defaults to input HAL file's tree root + #end if + > '$out_file' + ]]></command> + <inputs> + <expand macro="input_hal"/> + <expand macro="params_conditional_refGenome"/> + <conditional name="mode"> + <param name="export" type="select" label="Convert options"> + <option value="default" selected="true">Convert full reference genome (default)</option> + <option value="sequence">Convert a reference sequence (--refSequence)</option> + </param> + <when value="default"/> + <when value="sequence"> + <expand macro="params_sequence"/> + </when> + </conditional> + <expand macro="params_start"/> + <expand macro="params_length"/> + <conditional name="filter"> + <param name="option" type="select" label="Genomes to include in the output"> + <option value="" selected="true">All genomes (default)</option> + <option value="--targetGenomes">Specific target genomes (--targetGenomes)</option> + <option value="--rootGenome">Only genomes in the subtree to a root (--rootGenome)</option> + </param> + <when value=""/> + <when value="--targetGenomes"> + <expand macro="params_targetGenomes"/> + </when> + <when value="--rootGenome"> + <expand macro="params_rootGenome"/> + </when> + </conditional> + <param argument="--countDupes" type="boolean" truevalue="--countDupes" falsevalue="" checked="false" label="Count duplicates" help="Count every aligned position instead of counting unique genomes. This includes paralogous matches, so a genome can be counted multiple times. This will give the height of the MAF column created with hal2maf"/> + </inputs> + <outputs> + <data name="out_file" format="wig" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <output name="out_file" ftype="wig"> + <assert_contents> + <has_line line="fixedStep chrom=Genome_0_seq start=1 step=1"/> + <has_line line="3"/> + <has_line line="0"/> + <has_n_lines n="1759"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="mode"> + <param name="export" value="sequence"/> + <param name="sequence" value="Genome_0_seq"/> + </conditional> + <param name="start" value="10"/> + <param name="length" value="50"/> + <output name="out_file" ftype="wig"> + <assert_contents> + <has_line line="fixedStep chrom=Genome_0_seq start=11 step=1"/> + <has_line line="3"/> + <has_n_lines n="51"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <param name="countDupes" value="true"/> + <output name="out_file" ftype="wig"> + <assert_contents> + <has_line line="fixedStep chrom=Genome_0_seq start=1 step=1"/> + <has_line line="5"/> + <has_line line="10"/> + <has_line line="0"/> + <has_n_lines n="1759"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <conditional name="filter"> + <param name="option" value="--targetGenomes"/> + <param name="targetGenomes" value="Genome_1,Genome_2"/> + </conditional> + <output name="out_file" ftype="wig"> + <assert_contents> + <has_line line="fixedStep chrom=Genome_0_seq start=1 step=1"/> + <has_line line="2"/> + <has_line line="0"/> + <has_n_lines n="1759"/> + </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> + <output name="out_file" ftype="wig"> + <assert_contents> + <has_line line="fixedStep chrom=Genome_1_seq start=1 step=1"/> + <has_line line="2"/> + <has_line line="0"/> + <has_n_lines n="5473"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +halAlignmentDepth computes alignment depth across a reference genome from a HAL alignment. +The tool reports, for each base, how many genomes it aligns to. +By default, each genome is counted once per position, including ancestral genomes. +The result is written as a wiggle track. + ]]></help> + <expand macro="citation"/> + <expand macro="creator"/> +</tool> \ No newline at end of file