Mercurial > repos > genouest > helixer
comparison helixer.xml @ 1:7bc75dd0f782 draft
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/helixer commit e516933a2c3aa6bcd336a0b5c072893fe9019dd9
| author | genouest |
|---|---|
| date | Mon, 25 Sep 2023 12:47:12 +0000 |
| parents | 1b08e39cc52d |
| children | 7c1dc010a819 |
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| 0:1b08e39cc52d | 1:7bc75dd0f782 |
|---|---|
| 4 <macros> | 4 <macros> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 | 7 |
| 8 <requirements> | 8 <requirements> |
| 9 <expand macro="requirements" /> | 9 <expand macro="requirements"/> |
| 10 </requirements> | 10 </requirements> |
| 11 | 11 |
| 12 <command detect_errors="exit_code"><![CDATA[ | 12 <command detect_errors="exit_code"><![CDATA[ |
| 13 ## Not in $PATH in the docker image | |
| 14 ## Manage models with a data manager? | |
| 15 /usr/local/bin/fetch_helixer_models.py | |
| 16 | 13 |
| 17 && | 14 /usr/local/bin/fetch_helixer_models.py && |
| 18 | |
| 19 Helixer.py | 15 Helixer.py |
| 20 --fasta-path '$input' | 16 --fasta-path '$input' |
| 21 --species '$species' | 17 --species '$species' |
| 22 --lineage $lineage.lineages | 18 --lineage $lineage.lineages |
| 23 --gff-output-path '$output' | 19 --gff-output-path '$output' |
| 29 --overlap-offset $lineage.option_overlap.overlap_offset | 25 --overlap-offset $lineage.option_overlap.overlap_offset |
| 30 --overlap-core-length $lineage.option_overlap.overlap_core_length | 26 --overlap-core-length $lineage.option_overlap.overlap_core_length |
| 31 #else: | 27 #else: |
| 32 --no-overlap | 28 --no-overlap |
| 33 #end if | 29 #end if |
| 34 | 30 --batch-size $size |
| 35 --window-size $post_processing.window_size | 31 --window-size $post_processing.window_size |
| 36 --min-coding-length $post_processing.min_coding_length | 32 --min-coding-length $post_processing.min_coding_length |
| 37 --edge-threshold $post_processing.edge_threshold | 33 --edge-threshold $post_processing.edge_threshold |
| 38 --peak-threshold $post_processing.peak_threshold | 34 --peak-threshold $post_processing.peak_threshold |
| 39 ]]></command> | 35 ]]></command> |
| 66 <add value="_" /> | 62 <add value="_" /> |
| 67 </valid> | 63 </valid> |
| 68 </sanitizer> | 64 </sanitizer> |
| 69 <validator type="regex">[0-9a-zA-Z_]+</validator> | 65 <validator type="regex">[0-9a-zA-Z_]+</validator> |
| 70 </param> | 66 </param> |
| 71 | 67 <param name="size" argument="--batch-size" type="integer" value="8" label="Batch size" help="It may be necessary to reduce it if the GPU runs out of memory" /> |
| 72 <section name="post_processing" title="Post-processing"> | 68 <section name="post_processing" title="Post-processing"> |
| 73 <param argument="--window-size" type="integer" min="0" value="100" label="Window size" help="This determines the number of bases averaged during the sliding window approach"/> | 69 <param argument="--window-size" type="integer" min="0" value="100" label="Window size" help="This determines the number of bases averaged during the sliding window approach"/> |
| 74 <param argument="--edge-threshold" type="float" min="0" max="1" value="0.1" label="Edge threshold" help="This threshold specifies the genic score which defines the start / end boundaries of each candidate region"/> | 70 <param argument="--edge-threshold" type="float" min="0" max="1" value="0.1" label="Edge threshold" help="This threshold specifies the genic score which defines the start / end boundaries of each candidate region"/> |
| 75 <param argument="--peak-threshold" type="float" min="0" max="1" value="0.8" label="Peak threshold" help="This threshold specifies the minimum peak genic score required to accept the candidate region"/> | 71 <param argument="--peak-threshold" type="float" min="0" max="1" value="0.8" label="Peak threshold" help="This threshold specifies the minimum peak genic score required to accept the candidate region"/> |
| 76 <param argument="--min-coding-length" type="integer" min="0" value="100" label="Minimum coding length"/> | 72 <param argument="--min-coding-length" type="integer" min="0" value="100" label="Minimum coding length"/> |
| 80 <outputs> | 76 <outputs> |
| 81 <data name="output" format="gff3"> | 77 <data name="output" format="gff3"> |
| 82 </data> | 78 </data> |
| 83 </outputs> | 79 </outputs> |
| 84 <tests> | 80 <tests> |
| 85 <!-- Test for land_plant --> | |
| 86 <test expect_num_outputs="1"> | 81 <test expect_num_outputs="1"> |
| 87 <param name="input" value="sequence.fasta"/> | 82 <!-- Test for species and land_plant--> |
| 88 <conditional name="lineage"> | |
| 89 <param name="lineages" value="land_plant"/> | |
| 90 </conditional> | |
| 91 <output name="output" value="output.gff3" ftype="gff3" lines_diff="2" /> | |
| 92 </test> | |
| 93 <test expect_num_outputs="1"> | |
| 94 <!-- Test for species --> | |
| 95 <param name="input" value="sequence.fasta"/> | 83 <param name="input" value="sequence.fasta"/> |
| 96 <param name="species" value="Arabidopsis"/> | 84 <param name="species" value="Arabidopsis"/> |
| 97 <conditional name="lineage"> | 85 <conditional name="lineage"> |
| 98 <param name="lineages" value="land_plant"/> | 86 <param name="lineages" value="land_plant"/> |
| 99 </conditional> | 87 </conditional> |
| 100 <output name="output" value="ouput_species.gff3" ftype="gff3" lines_diff="2" /> | 88 <param name="size" value="8"/> |
| 89 <output name="output" value="ouput_species.gff3" ftype="gff3" compare="sim_size" delta="100"/> | |
| 90 </test> | |
| 91 <test expect_num_outputs="1"> | |
| 92 <!-- Test for vertebrates--> | |
| 93 <param name="input" value="sequence.fasta"/> | |
| 94 <conditional name="lineage"> | |
| 95 <param name="lineages" value="vertebrate"/> | |
| 96 </conditional> | |
| 97 <param name="size" value="8"/> | |
| 98 <output name="output" value="vertebrate.gff3" ftype="gff3" lines_diff="2"/> | |
| 99 </test> | |
| 100 <test expect_num_outputs="1"> | |
| 101 <!-- Test for invertebrates--> | |
| 102 <param name="input" value="sequence.fasta"/> | |
| 103 <conditional name="lineage"> | |
| 104 <param name="lineages" value="invertebrate"/> | |
| 105 </conditional> | |
| 106 <param name="size" value="8"/> | |
| 107 <output name="output" value="invertebrate.gff3" ftype="gff3" lines_diff="2"/> | |
| 108 </test> | |
| 109 <test expect_num_outputs="1"> | |
| 110 <!-- Test for fungi--> | |
| 111 <param name="input" value="sequence.fasta"/> | |
| 112 <conditional name="lineage"> | |
| 113 <param name="lineages" value="fungi"/> | |
| 114 </conditional> | |
| 115 <param name="size" value="8"/> | |
| 116 <output name="output" value="fungi.gff3" ftype="gff3" lines_diff="2"/> | |
| 101 </test> | 117 </test> |
| 102 </tests> | 118 </tests> |
| 103 | |
| 104 | 119 |
| 105 <help><![CDATA[ | 120 <help><![CDATA[ |
| 106 Helixer_: Gene calling with Deep Neural Networks. | 121 Helixer_: Gene calling with Deep Neural Networks. |
| 107 | 122 |
| 108 .. _Helixer: https://github.com/weberlab-hhu/Helixer | 123 .. _Helixer: https://github.com/weberlab-hhu/Helixer |