Mercurial > repos > iuc > funannotate_sort
comparison funannotate_sort.xml @ 0:998b719a94cb draft
"planemo upload commit 9613152729099079c7465c3d5d42005ef22ca91e"
| author | iuc |
|---|---|
| date | Thu, 26 Aug 2021 06:56:18 +0000 |
| parents | |
| children | 520e30695ec3 |
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| -1:000000000000 | 0:998b719a94cb |
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| 1 <tool id="funannotate_sort" name="Sort assembly" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> | |
| 2 <description></description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <requirements> | |
| 7 <expand macro="requirements" /> | |
| 8 </requirements> | |
| 9 <version_command>funannotate check --show-versions</version_command> | |
| 10 <command><![CDATA[ | |
| 11 funannotate sort | |
| 12 --input '${input}' | |
| 13 --out '${output}' | |
| 14 --base '${base}' | |
| 15 --minlen ${minlen} | |
| 16 ]]></command> | |
| 17 <inputs> | |
| 18 <param argument="--input" type="data" format="fasta" label="Assembly to sort" /> | |
| 19 | |
| 20 <param argument="--base" type="text" value="scaffold" label="Base name to relabel contigs"> | |
| 21 <validator type="regex" message="No special characters allowed">^(?:\w+)?$</validator> | |
| 22 </param> | |
| 23 <param argument="--minlen" type="integer" value="0" label="Shorter contigs are discarded" /> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data name='output' format='fasta' label="${tool.name} on ${on_string}: sorted assembly" /> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="input" value="genome.fa" /> | |
| 31 <output name="output"> | |
| 32 <assert_contents> | |
| 33 <has_text text=">scaffold_1" /> | |
| 34 <has_text text=">scaffold_4" /> | |
| 35 </assert_contents> | |
| 36 </output> | |
| 37 </test> | |
| 38 <test> | |
| 39 <param name="input" value="genome.fa" /> | |
| 40 <param name="base" value="something" /> | |
| 41 <param name="minlen" value="2100" /> | |
| 42 <output name="output"> | |
| 43 <assert_contents> | |
| 44 <has_text text=">something_1" /> | |
| 45 <not_has_text text=">something_4" /> | |
| 46 </assert_contents> | |
| 47 </output> | |
| 48 </test> | |
| 49 </tests> | |
| 50 <help><![CDATA[ | |
| 51 Funannotate_ sort | |
| 52 ----------------- | |
| 53 | |
| 54 Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). | |
| 55 | |
| 56 This script sorts the input contigs by size (longest->shortest) and then relabels | |
| 57 the contigs with a simple name (e.g. scaffold_1). Augustus can have problems with | |
| 58 some complicated contig names. | |
| 59 | |
| 60 .. _Funannotate: http://funannotate.readthedocs.io | |
| 61 ]]></help> | |
| 62 <expand macro="citations" /> | |
| 63 </tool> |