Mercurial > repos > iuc > hal_halalignedextract
comparison hal_halAlignedExtract.xml @ 0:4638a5ff6186 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac
| author | iuc |
|---|---|
| date | Fri, 06 Feb 2026 10:36:30 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:4638a5ff6186 |
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| 1 <tool id="hal_halalignedextract" name="halAlignedExtract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
| 2 <description>extracts aligned regions of a genome with its parent</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 halAlignedExtract | |
| 10 $complement | |
| 11 $viewParentCoords | |
| 12 '$input_hal' '$genome' > '$out_file' | |
| 13 ]]></command> | |
| 14 <inputs> | |
| 15 <expand macro="input_hal"/> | |
| 16 <expand macro="params_genomeNoRoot"/> | |
| 17 <param argument="--viewParentCoords" type="boolean" truevalue="--viewParentCoords" falsevalue="" checked="false" label="View parent coordinates" help="View the corresponding parent coordinates for aligned regions"/> | |
| 18 <param argument="--complement" type="boolean" truevalue="--complement" falsevalue="" checked="false" label="Complement regions" help="Extract the regions of the genome that are *unaligned* to the parent. i.e. all intervals that are not returned with the default setting"/> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data name="out_file" format="bed" label="${tool.name} on ${on_string}"/> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test expect_num_outputs="1"> | |
| 25 <param name="input_hal" value="halTest.hal"/> | |
| 26 <param name="genome" value="Genome_1"/> | |
| 27 <param name="viewParentCoords" value="true"/> | |
| 28 <output name="out_file" ftype="bed"> | |
| 29 <assert_contents> | |
| 30 <has_line line="Genome_1_seq	0	293	Genome_0_seq	0	293	+"/> | |
| 31 <has_line line="Genome_1_seq	2637	2930	Genome_0_seq	293	586	+"/> | |
| 32 <has_line line="Genome_1_seq	5135	5274	Genome_0_seq	1033	1172	+"/> | |
| 33 <has_n_lines n="26"/> | |
| 34 </assert_contents> | |
| 35 </output> | |
| 36 </test> | |
| 37 <test expect_num_outputs="1"> | |
| 38 <param name="input_hal" value="halTest.hal"/> | |
| 39 <param name="genome" value="Genome_1"/> | |
| 40 <param name="complement" value="true"/> | |
| 41 <output name="out_file" ftype="bed"> | |
| 42 <assert_contents> | |
| 43 <has_line line="Genome_1_seq	1465	1758"/> | |
| 44 <has_line line="Genome_1_seq	5274	5472"/> | |
| 45 <has_n_lines n="4"/> | |
| 46 </assert_contents> | |
| 47 </output> | |
| 48 </test> | |
| 49 </tests> | |
| 50 <help><![CDATA[ | |
| 51 halAlignedExtract scans a given genome from an input HAL file and extracts regions that are aligned to its direct parent genome. | |
| 52 The tool reports all aligned blocks by default. Optionally, it can report the complementary set of regions that are not aligned to the parent. | |
| 53 The output is written as BED intervals. | |
| 54 ]]></help> | |
| 55 <expand macro="citation"/> | |
| 56 <expand macro="creator"/> | |
| 57 </tool> |