Mercurial > repos > iuc > hal_halpctid

comparison hal_halPctId.xml @ 2:95f0cb8ccfe1 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 15:21:14 +0000
parents 07c1e49a89de
children
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equal deleted inserted replaced
1:3abff47d131b 2:95f0cb8ccfe1
9 set -o pipefail; ## Sets the pipeline’s exit code to halPctId’s on failure. 9 set -o pipefail; ## Sets the pipeline’s exit code to halPctId’s on failure.
10 halPctId 10 halPctId
11 --numSamples $numSamples 11 --numSamples $numSamples
12 --seed $seed 12 --seed $seed
13 ## Pipes output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree. 13 ## Pipes output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
14 '$input_hal' '$refGenome' | tr ',' '\t' > '$out_file' 14 '$input_hal' '$refGenome' | sed $'s/, */\t/g' > '$out_file'
15 ]]></command> 15 ]]></command>
16 <inputs> 16 <inputs>
17 <expand macro="input_hal"/> 17 <expand macro="input_hal"/>
18 <expand macro="params_refGenome"/> 18 <expand macro="params_refGenome"/>
19 <expand macro="params_numSamples"/> 19 <expand macro="params_numSamples"/>
27 <param name="input_hal" value="halTest.hal"/> 27 <param name="input_hal" value="halTest.hal"/>
28 <param name="refGenome" value="Genome_1"/> 28 <param name="refGenome" value="Genome_1"/>
29 <param name="seed" value="100"/> 29 <param name="seed" value="100"/>
30 <output name="out_file" ftype="tabular"> 30 <output name="out_file" ftype="tabular">
31 <assert_contents> 31 <assert_contents>
32 <has_line line="Genome&#009; IdenticalSites&#009; AlignedSites&#009; PercentIdentity"/> 32 <has_line line="Genome&#009;IdenticalSites&#009;AlignedSites&#009;PercentIdentity"/>
33 <has_line line="Genome_1&#009; 856475&#009; 856475&#009; 100"/> 33 <has_line line="Genome_1&#009;856475&#009;856475&#009;100"/>
34 <has_line line="Genome_2&#009; 374132&#009; 374132&#009; 100"/> 34 <has_line line="Genome_2&#009;374132&#009;374132&#009;100"/>
35 <has_n_lines n="4"/> 35 <has_n_lines n="4"/>
36 </assert_contents> 36 </assert_contents>
37 </output> 37 </output>
38 </test> 38 </test>
39 <test expect_num_outputs="1"> 39 <test expect_num_outputs="1">
41 <param name="refGenome" value="Genome_1"/> 41 <param name="refGenome" value="Genome_1"/>
42 <param name="numSamples" value="1000"/> 42 <param name="numSamples" value="1000"/>
43 <param name="seed" value="100"/> 43 <param name="seed" value="100"/>
44 <output name="out_file" ftype="tabular"> 44 <output name="out_file" ftype="tabular">
45 <assert_contents> 45 <assert_contents>
46 <has_line line="Genome&#009; IdenticalSites&#009; AlignedSites&#009; PercentIdentity"/> 46 <has_line line="Genome&#009;IdenticalSites&#009;AlignedSites&#009;PercentIdentity"/>
47 <has_line line="Genome_1&#009; 839&#009; 839&#009; 100"/> 47 <has_line line="Genome_1&#009;839&#009;839&#009;100"/>
48 <has_line line="Genome_2&#009; 339&#009; 339&#009; 100"/> 48 <has_line line="Genome_2&#009;339&#009;339&#009;100"/>
49 <has_n_lines n="4"/> 49 <has_n_lines n="4"/>
50 </assert_contents> 50 </assert_contents>
51 </output> 51 </output>
52 </test> 52 </test>
53 </tests> 53 </tests>