Mercurial > repos > iuc > hal_halsnps

comparison hal_halSnps.xml @ 2:9c83aa0e3e6a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 30ac0af6dfa729277011bcd73cd5560efa03fb97
author iuc
date Wed, 18 Mar 2026 15:21:28 +0000
parents 50336dc82da7
children
comparison
equal deleted inserted replaced
1:50336dc82da7 2:9c83aa0e3e6a
14 --refSequence '$mode.sequence' 14 --refSequence '$mode.sequence'
15 #end if 15 #end if
16 --start $start 16 --start $start
17 --length $length 17 --length $length
18 --minSpeciesForSnp $minSpeciesForSnp 18 --minSpeciesForSnp $minSpeciesForSnp
19 #if $tsv:
20 --tsv '$out_file_detail'
21 #end if
19 $noDupes 22 $noDupes
20 $unique 23 $unique
21 '$input_hal' '$refGenome' '$targetGenomes' 24 '$input_hal' '$refGenome' '$targetGenomes'
22 | tr ' ' '\t' ## Pipes specific output to replace space with tabs. Output is mostly numerical, and Genome names should not contain spaces 25 | tr ' ' '\t' ## Pipes specific output to replace space with tabs. Output is mostly numerical, and Genome names should not contain spaces
23 >> '$out_file' 26 >> '$out_file'
37 </when> 40 </when>
38 </conditional> 41 </conditional>
39 <expand macro="params_start"/> 42 <expand macro="params_start"/>
40 <expand macro="params_length"/> 43 <expand macro="params_length"/>
41 <param argument="--noDupes" type="boolean" truevalue="--noDupes" falsevalue="" checked="false" label="No duplicates" help="Do not consider paralogies while mapping"/> 44 <param argument="--noDupes" type="boolean" truevalue="--noDupes" falsevalue="" checked="false" label="No duplicates" help="Do not consider paralogies while mapping"/>
45 <param argument="--tsv" type="boolean" truevalue="--tsv" falsevalue="" checked="false" label="Detailed SNPs file" help="Create a detailed file containing base assignments for each genome at SNP locations"/>
42 <param argument="--minSpeciesForSnp" type="integer" min="1" value="1" label="Minimum number of species" help="Minimum number of species that must have a different base than the reference for a SNP to be reported in the output"/> 46 <param argument="--minSpeciesForSnp" type="integer" min="1" value="1" label="Minimum number of species" help="Minimum number of species that must have a different base than the reference for a SNP to be reported in the output"/>
43 <param argument="--unique" type="boolean" truevalue="--unique" falsevalue="" checked="false" label="Unique" help="Whether to ignore columns that are not canonical on the reference genome"/> 47 <param argument="--unique" type="boolean" truevalue="--unique" falsevalue="" checked="false" label="Unique" help="Whether to ignore columns that are not canonical on the reference genome"/>
44 </inputs> 48 </inputs>
45 <outputs> 49 <outputs>
46 <data name="out_file" format="tabular" label="${tool.name} on ${on_string}"/> 50 <data name="out_file" format="tabular" label="${tool.name} on ${on_string}"/>
51 <data name="out_file_detail" format="tabular" label="${tool.name} on ${on_string}: Detailed SNPs file">
52 <filter>tsv</filter>
53 </data>
47 </outputs> 54 </outputs>
48 <tests> 55 <tests>
49 <test expect_num_outputs="1"> 56 <test expect_num_outputs="1">
50 <param name="input_hal" value="halTest.hal"/> 57 <param name="input_hal" value="halTest.hal"/>
51 <param name="refGenome" value="Genome_0"/> 58 <param name="refGenome" value="Genome_0"/>
105 <has_line line="Genome_2&#009;0&#009;283"/> 112 <has_line line="Genome_2&#009;0&#009;283"/>
106 <has_n_lines n="4"/> 113 <has_n_lines n="4"/>
107 </assert_contents> 114 </assert_contents>
108 </output> 115 </output>
109 </test> 116 </test>
117 <test expect_num_outputs="2">
118 <param name="input_hal" value="halTestExtended.hal"/>
119 <param name="refGenome" value="Genome_0"/>
120 <param name="targetGenomes" value="Genome_1,Insert"/>
121 <param name="tsv" value="true"/>
122 <output name="out_file" ftype="tabular">
123 <assert_contents>
124 <has_line line="targetGenome&#009;totalSnps&#009;totalCleanOrthologousPairs"/>
125 <has_line line="Genome_1&#009;0&#009;0"/>
126 <has_line line="Insert&#009;32&#009;586"/>
127 <has_n_lines n="3"/>
128 </assert_contents>
129 </output>
130 <output name="out_file_detail" ftype="tabular">
131 <assert_contents>
132 <has_line line="refSequence&#009;refPosition&#009;Genome_0&#009;Genome_1&#009;Insert"/>
133 <has_line line="Genome_0_seq&#009;10&#009;G&#009;&#009;C"/>
134 <has_n_lines n="33"/>
135 </assert_contents>
136 </output>
137 </test>
110 </tests> 138 </tests>
111 <help><![CDATA[ 139 <help><![CDATA[
112 halSnps counts SNPs between orthologous positions across multiple genomes in a HAL alignment. 140 halSnps counts SNPs between orthologous positions across multiple genomes in a HAL alignment.
113 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. 141 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.
114 ]]></help> 142 ]]></help>