Mercurial > repos > iuc > hal_halpctid
comparison hal_halPctId.xml @ 0:fcc762afb884 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 10:32:49 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:fcc762afb884 |
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| 1 <tool id="hal_halpctid" name="halPctId" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
| 2 <description>calculates % identity by sampling bases</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <expand macro="stdio"/> | |
| 8 <command detect_errors="aggressive"><![CDATA[ | |
| 9 set -o pipefail; ## Sets the pipeline’s exit code to halPctId’s on failure. | |
| 10 halPctId | |
| 11 --numSamples $numSamples | |
| 12 --seed $seed | |
| 13 ## Pipes output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree. | |
| 14 '$input_hal' '$refGenome' | tr ',' '\t' > '$out_file' | |
| 15 ]]></command> | |
| 16 <inputs> | |
| 17 <expand macro="input_hal"/> | |
| 18 <expand macro="params_refGenome"/> | |
| 19 <expand macro="params_numSamples"/> | |
| 20 <expand macro="params_seed"/> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data name="out_file" format="tabular" label="${tool.name} on ${on_string}: ${refGenome}"/> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test expect_num_outputs="1"> | |
| 27 <param name="input_hal" value="halTest.hal"/> | |
| 28 <param name="refGenome" value="Genome_1"/> | |
| 29 <param name="seed" value="100"/> | |
| 30 <output name="out_file" ftype="tabular"> | |
| 31 <assert_contents> | |
| 32 <has_line line="Genome	 IdenticalSites	 AlignedSites	 PercentIdentity"/> | |
| 33 <has_line line="Genome_1	 856475	 856475	 100"/> | |
| 34 <has_line line="Genome_2	 374132	 374132	 100"/> | |
| 35 <has_n_lines n="4"/> | |
| 36 </assert_contents> | |
| 37 </output> | |
| 38 </test> | |
| 39 <test expect_num_outputs="1"> | |
| 40 <param name="input_hal" value="halTest.hal"/> | |
| 41 <param name="refGenome" value="Genome_1"/> | |
| 42 <param name="numSamples" value="1000"/> | |
| 43 <param name="seed" value="100"/> | |
| 44 <output name="out_file" ftype="tabular"> | |
| 45 <assert_contents> | |
| 46 <has_line line="Genome	 IdenticalSites	 AlignedSites	 PercentIdentity"/> | |
| 47 <has_line line="Genome_1	 839	 839	 100"/> | |
| 48 <has_line line="Genome_2	 339	 339	 100"/> | |
| 49 <has_n_lines n="4"/> | |
| 50 </assert_contents> | |
| 51 </output> | |
| 52 </test> | |
| 53 </tests> | |
| 54 <help><![CDATA[ | |
| 55 halPctId computes percent identity (% ID) for a reference genome in a HAL alignment by randomly sampling bases. | |
| 56 It takes a HAL file and a reference genome name as input and outputs a table summarizing the result. | |
| 57 A random seed can be set for reproducibility. | |
| 58 ]]></help> | |
| 59 <expand macro="citation"/> | |
| 60 <expand macro="creator"/> | |
| 61 </tool> |