Mercurial > repos > iuc > hal_halsnps
diff hal_halSnps.xml @ 0:116020f2c8f3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac
| author | iuc |
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| date | Fri, 06 Feb 2026 10:35:08 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hal_halSnps.xml Fri Feb 06 10:35:08 2026 +0000 @@ -0,0 +1,117 @@ +<tool id="hal_halsnps" name="halSnps" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>counts SNPs between orthologous positions in multiple genomes</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command detect_errors="aggressive"><![CDATA[ + set -o pipefail; ## Sets the pipeline’s exit code to halSnps on failure. + ( ## echo headers for specific numerical data + echo -e "targetGenome\ttotalSnps\ttotalCleanOrthologousPairs"; + halSnps + #if $mode.export == 'sequence': + --refSequence '$mode.sequence' + #end if + --start $start + --length $length + --minSpeciesForSnp $minSpeciesForSnp + $noDupes + $unique + '$input_hal' '$refGenome' '$targetGenomes' + | tr ' ' '\t' ## Pipes specific output to replace space with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree. + ) > '$out_file' + ]]></command> + <inputs> + <expand macro="input_hal"/> + <expand macro="params_refGenome"/> + <expand macro="params_targetGenomes"/> + <conditional name="mode"> + <param name="export" type="select" label="Process options"> + <option value="default" selected="true">Process all sequences (default)</option> + <option value="sequence">Process a specific sequence (--refSequence)</option> + </param> + <when value="default"/> + <when value="sequence"> + <expand macro="params_sequence"/> + </when> + </conditional> + <expand macro="params_start"/> + <expand macro="params_length"/> + <param argument="--noDupes" type="boolean" truevalue="--noDupes" falsevalue="" checked="false" label="No duplicates" help="Do not consider paralogies while mapping"/> + <param argument="--minSpeciesForSnp" type="integer" min="1" value="1" label="Minimum number of species" help="Minimum number of species that must have a different base than the reference for a SNP to be reported in the output"/> + <param argument="--unique" type="boolean" truevalue="--unique" falsevalue="" checked="false" label="Unique" help="Whether to ignore columns that are not canonical on the reference genome"/> + </inputs> + <outputs> + <data name="out_file" format="tabular" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <param name="refGenome" value="Genome_0"/> + <param name="targetGenomes" value="Genome_0,Genome_1,Genome_2"/> + <output name="out_file" ftype="tabular"> + <assert_contents> + <has_line line="targetGenome	totalSnps	totalCleanOrthologousPairs"/> + <has_line line="Genome_0	0	1758"/> + <has_line line="Genome_2	0	586"/> + <has_n_lines n="4"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <param name="refGenome" value="Genome_0"/> + <param name="targetGenomes" value="Genome_0,Genome_1,Genome_2"/> + <param name="noDupes" value="true"/> + <output name="out_file" ftype="tabular"> + <assert_contents> + <has_line line="targetGenome	totalSnps	totalCleanOrthologousPairs"/> + <has_line line="Genome_0	0	0"/> + <has_line line="Genome_2	0	1465"/> + <has_n_lines n="4"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <param name="refGenome" value="Genome_0"/> + <param name="targetGenomes" value="Genome_0,Genome_1,Genome_2"/> + <param name="start" value="10"/> + <param name="length" value="50"/> + <output name="out_file" ftype="tabular"> + <assert_contents> + <has_line line="targetGenome	totalSnps	totalCleanOrthologousPairs"/> + <has_line line="Genome_0	0	50"/> + <has_line line="Genome_2	0	50"/> + <has_n_lines n="4"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_hal" value="halTest.hal"/> + <param name="refGenome" value="Genome_0"/> + <param name="targetGenomes" value="Genome_0,Genome_1,Genome_2"/> + <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="500"/> + <output name="out_file" ftype="tabular"> + <assert_contents> + <has_line line="targetGenome	totalSnps	totalCleanOrthologousPairs"/> + <has_line line="Genome_0	0	500"/> + <has_line line="Genome_2	0	283"/> + <has_n_lines n="4"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +halSnps counts SNPs between orthologous positions across multiple genomes in a HAL alignment. +The tool compares each position in a reference genome against one or more target genomes and reports how many SNPs occur, along with the number of clean orthologous positions examined. + ]]></help> + <expand macro="citation"/> + <expand macro="creator"/> +</tool> \ No newline at end of file