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comparison hal_halCoverage.xml @ 2:6ee278f53917 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 15:17:13 +0000
parents 2ead05695f9f
children
comparison
equal deleted inserted replaced
1:0f5bcf7e18a7 2:6ee278f53917
10 halCoverage 10 halCoverage
11 --numSamples $numSamples 11 --numSamples $numSamples
12 --seed $seed 12 --seed $seed
13 $bySequence 13 $bySequence
14 ## Pipes output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree. 14 ## Pipes output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
15 '$input_hal' '$refGenome' | tr ',' '\t' > '$out_file' 15 '$input_hal' '$refGenome' | sed $'s/, */\t/g' > '$out_file'
16 ]]></command> 16 ]]></command>
17 <inputs> 17 <inputs>
18 <expand macro="input_hal"/> 18 <expand macro="input_hal"/>
19 <expand macro="params_refGenome"/> 19 <expand macro="params_refGenome"/>
20 <expand macro="params_numSamples"/> 20 <expand macro="params_numSamples"/>
29 <param name="input_hal" value="halTest.hal"/> 29 <param name="input_hal" value="halTest.hal"/>
30 <param name="refGenome" value="Genome_1"/> 30 <param name="refGenome" value="Genome_1"/>
31 <param name="seed" value="100"/> 31 <param name="seed" value="100"/>
32 <output name="out_file" ftype="tabular"> 32 <output name="out_file" ftype="tabular">
33 <assert_contents> 33 <assert_contents>
34 <has_line line="Genome&#009; sitesCovered1Times&#009; sitesCovered2Times&#009; sitesCovered3Times&#009; sitesCovered4Times&#009; sitesCovered5Times"/> 34 <has_line line="Genome&#009;sitesCovered1Times&#009;sitesCovered2Times&#009;sitesCovered3Times&#009;sitesCovered4Times&#009;sitesCovered5Times"/>
35 <has_line line="Genome_2&#009; 856475&#009; 482343&#009; 482343&#009; 214021&#009; 0"/> 35 <has_line line="Genome_2&#009;856475&#009;482343&#009;482343&#009;214021&#009;0"/>
36 <has_n_lines n="4"/> 36 <has_n_lines n="4"/>
37 </assert_contents> 37 </assert_contents>
38 </output> 38 </output>
39 </test> 39 </test>
40 <test expect_num_outputs="1"> 40 <test expect_num_outputs="1">
42 <param name="refGenome" value="Genome_1"/> 42 <param name="refGenome" value="Genome_1"/>
43 <param name="numSamples" value="1000"/> 43 <param name="numSamples" value="1000"/>
44 <param name="seed" value="100"/> 44 <param name="seed" value="100"/>
45 <output name="out_file" ftype="tabular"> 45 <output name="out_file" ftype="tabular">
46 <assert_contents> 46 <assert_contents>
47 <has_line line="Genome&#009; sitesCovered1Times&#009; sitesCovered2Times&#009; sitesCovered3Times&#009; sitesCovered4Times&#009; sitesCovered5Times"/> 47 <has_line line="Genome&#009;sitesCovered1Times&#009;sitesCovered2Times&#009;sitesCovered3Times&#009;sitesCovered4Times&#009;sitesCovered5Times"/>
48 <has_line line="Genome_2&#009; 839&#009; 500&#009; 500&#009; 233&#009; 0"/> 48 <has_line line="Genome_2&#009;839&#009;500&#009;500&#009;233&#009;0"/>
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 <test expect_num_outputs="1"> 53 <test expect_num_outputs="1">
55 <param name="refGenome" value="Genome_1"/> 55 <param name="refGenome" value="Genome_1"/>
56 <param name="bySequence" value="true"/> 56 <param name="bySequence" value="true"/>
57 <param name="seed" value="100"/> 57 <param name="seed" value="100"/>
58 <output name="out_file" ftype="tabular"> 58 <output name="out_file" ftype="tabular">
59 <assert_contents> 59 <assert_contents>
60 <has_line line="Genome&#009; sitesCovered1Times&#009; sitesCovered2Times&#009; sitesCovered3Times&#009; sitesCovered4Times&#009; sitesCovered5Times"/> 60 <has_line line="Genome&#009;sitesCovered1Times&#009;sitesCovered2Times&#009;sitesCovered3Times&#009;sitesCovered4Times&#009;sitesCovered5Times"/>
61 <has_line line="Genome_2&#009; 856475&#009; 482343&#009; 482343&#009; 214021&#009; 0"/> 61 <has_line line="Genome_2&#009;856475&#009;482343&#009;482343&#009;214021&#009;0"/>
62 <has_line line="Coverage on Genome_1_seq"/> 62 <has_line line="Coverage on Genome_1_seq"/>
63 <has_n_lines n="9"/> 63 <has_n_lines n="9"/>
64 </assert_contents> 64 </assert_contents>
65 </output> 65 </output>
66 </test> 66 </test>