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abretaudabretaud
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Merge pull request #60 from rlibouba/update_helixer_036
Helixer update (version 0.3.6)
2 parents 43caacb + 5023f87 commit 04e19d1

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Lines changed: 56 additions & 68 deletions

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‎tools/helixer/helixer.xml‎

Lines changed: 52 additions & 62 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
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<?xml version="1.0"?>
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<tool id="helixer" name="Helixer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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<tool id="helixer" name="Helixer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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<description>gene calling</description>
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<macros>
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<import>macros.xml</import>
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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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/usr/local/bin/fetch_helixer_models.py &&
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Helixer.py
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--fasta-path '$input'
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--species '$species'
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--gff-output-path '$output'
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--temporary-dir ./
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#set default_subsequence_length = {"fungi": 21384, "land_plant": 106920, "invertebrate": 213840, "vertebrate": 213840}
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#set subsequence_len = default_subsequence_length.get(str($lineages))
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#set default_overlap_offset = {"fungi": 10692, "land_plant": 53460, "invertebrate": 106920, "vertebrate": 106920}
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#set overlap_off = default_overlap_offset.get(str($lineages))
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#set default_overlap_core_length = {"fungi": 16038, "land_plant": 80190, "invertebrate": 160380, "vertebrate": 160380}
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#set overlap_core_len = default_overlap_core_length.get(str($lineages))
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/usr/local/bin/fetch_helixer_models.py &&
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#if str($input_model) != "" and str($input_model) != "None":
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--model-filepath '$input_model'
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--subsequence-length '$subsequence_length'
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Helixer.py
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--fasta-path '$input'
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--species '$species'
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--gff-output-path '$output'
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#set default_subsequence_length = {"fungi": 21384, "land_plant": 106920, "invertebrate": 213840, "vertebrate": 213840}
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#set subsequence_len = default_subsequence_length.get(str($lineages))
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#set default_overlap_offset = {"fungi": 10692, "land_plant": 53460, "invertebrate": 106920, "vertebrate": 106920}
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#set overlap_off = default_overlap_offset.get(str($lineages))
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#set default_overlap_core_length = {"fungi": 16038, "land_plant": 80190, "invertebrate": 160380, "vertebrate": 160380}
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#set overlap_core_len = default_overlap_core_length.get(str($lineages))
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#else:
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--lineage '$lineages'
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#if str($subsequence_length) == "":
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--subsequence-length '$subsequence_len'
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#else:
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#if str($input_model) != "" and str($input_model) != "None":
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--model-filepath '$input_model'
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--subsequence-length '$subsequence_length'
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#end if
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#if str($option_overlap.use_overlap) == "true":
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#if str($option_overlap.overlap_offset) == "":
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--overlap-offset '$overlap_off'
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#else:
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--lineage '$lineages'
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#if str($subsequence_length) == "":
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--subsequence-length '$subsequence_len'
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#else:
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--overlap-offset '$overlap_offset'
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--subsequence-length '$subsequence_length'
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#end if
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#if str($option_overlap.overlap_core_length) == "":
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--overlap-core-length '$overlap_core_len'
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#else:
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--overlap-core-length '$overlap_core_length'
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#if str($option_overlap.use_overlap) == "true":
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#if str($option_overlap.overlap_offset) == "":
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--overlap-offset '$overlap_off'
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#else:
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--overlap-offset '$overlap_offset'
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#end if
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#if str($option_overlap.overlap_core_length) == "":
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--overlap-core-length '$overlap_core_len'
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#else:
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--overlap-core-length '$overlap_core_length'
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#end if
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#end if
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#end if
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#end if
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--batch-size $size
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--window-size $post_processing.window_size
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--min-coding-length $post_processing.min_coding_length
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--edge-threshold $post_processing.edge_threshold
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--peak-threshold $post_processing.peak_threshold
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--batch-size $size
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--window-size $post_processing.window_size
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--min-coding-length $post_processing.min_coding_length
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--edge-threshold $post_processing.edge_threshold
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--peak-threshold $post_processing.peak_threshold
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#if $write_by:
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--write-by $write_by
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#end if
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#if $no_multiprocess == "true":
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--no-multiprocess
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#end if
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]]></command>
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<inputs>
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<param argument="--fasta-path" name="input" type="data" format="fasta,fasta.gz" label="Genomic sequence"></param>
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<param argument="--model-filepath" optional="true" name="input_model" type="data" format="h5" label="Lineage model" help="Import your lineage model to replace the default lineage. Please enter a value for the --subsequence_length parameter."></param>
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<param argument="--lineage" name="lineages" type="select" label="Available lineages" help="Choose the model to use for the annotation">
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<option value="land_plant">land plant</option>
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<option value="vertebrate">vertebrate</option>
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</when>
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<when value="false"/>
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</conditional>
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<param name="write_by" type="integer" value="20000000" optional="true" label="Number of base pairs per super-chunk" help="For lower memory consumption, consider setting a lower number. Please note that this value must be greater than or equal to « --subsequence-length »"/>
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<param name="no_multiprocess" type="boolean" truevalue="--no_multiprocess" falsevalue="" checked="false" label="Do you want to disable multiprocessing?" help="By disabling it, you will reduce RAM consumption. You can do this especially on small genomes."/>
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</inputs>
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<outputs>
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<test expect_num_outputs="1">
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<!-- Test for species and land_plant-->
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<param name="input" value="sequence.fasta"/>
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<param name="lineages" value="land_plant"/>
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<param name="lineages" value="vertebrate"/>
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<param name="species" value="Arabidopsis"/>
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<param name="size" value="8"/>
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<param name="subsequence_length" value=""/>
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<param name="overlap_offset" value=""/>
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<param name="overlap_core_length" value=""/>
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</conditional>
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<output name="output" value="ouput_species.gff3" ftype="gff3" compare="sim_size" delta="100"/>
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<output name="output" value="ouput_species.gff3" ftype="gff3" compare="sim_size" delta="10000"/>
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</test>
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<test expect_num_outputs="1">
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</conditional>
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<output name="output" value="vertebrate.gff3" ftype="gff3" lines_diff="2"/>
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</test>
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<test expect_failure="true">
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<!-- Test for model-filepath -->
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<param name="input" value="sequence.fasta"/>
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<param name="input_model" value="test.h5"/>
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<param name="size" value="8"/>
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<param name="size" value="8"/>
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<param name="subsequence_length" value="1000"/>
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<section name="post_processing">
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<param name="window_size" value="100"/>
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<param name="edge_threshold" value="0.1"/>
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<param name="peak_threshold" value="0.8"/>
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<param name="min_coding_length" value="100"/>
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</section>
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<conditional name="option_overlap">
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<param name="use_overlap" value="true"/>
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<param name="overlap_offset" value=""/>
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<param name="overlap_core_length" value=""/>
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</conditional>
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</test>
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</tests>
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<help><![CDATA[

‎tools/helixer/macros.xml‎

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Original file line numberDiff line numberDiff line change
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<macros>
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<token name="@TOOL_VERSION@">0.3.3</token>
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<token name="@VERSION_SUFFIX@">1</token>
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<token name="@TOOL_VERSION@">0.3.6</token>
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<token name="@VERSION_SUFFIX@">0</token>
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<xml name="citation">
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</xml>
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<xml name="requirements">
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<container type="docker">gglyptodon/helixer-docker:helixer_v@TOOL_VERSION@_cuda_11.8.0-cudnn8</container>
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<container type="docker">gglyptodon/helixer-docker:helixer_v@TOOL_VERSION@_cuda_12.2.2-cudnn8_1</container>
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</xml>
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</macros>
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</macros>

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