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nsoranzonsoranzo
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Fix linting issues
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-26
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9 files changed

+50
-26
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‎data_managers/data_manager_pangolin_data/data_manager/pangolin_data_dm.xml‎

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</conditional>
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<conditional name="pangolin_constellations">
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<param name="enable" value="no" />
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<param name="compatibility_file" ftype="csv" value="data_compatibility.csv" />
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<param name="versions" value="0.0.40" />
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</conditional>
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<conditional name="pangolin_assignment">
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<param name="enable" value="no" />

‎tools/fasta_stats/.shed.yml‎

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categories:
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- Sequence Analysis
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description: Display summary statistics for a fasta file.
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description: Display summary statistics for a FASTA file.
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homepage_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats/
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long_description: |
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This tool generates statistics for a FASTA file: a general summary and an
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optional gap stats file.
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name: fasta_stats
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owner: iuc
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remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats

‎tools/genebed_maf_to_fasta/.shed.yml‎

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owner: iuc
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description: Stitch gene blocks given a set of coding exon intervals
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homepage_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta/
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long_description: |
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This tool takes a list of coding exons (in the Gene BED format) and a MAF
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alignment file, finds all MAF blocks that overlap the coding regions, sorts
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MAF blocks by alignment score, stitches blocks together resolving overlaps
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based on alignment score, and finally outputs the stitched alignments in FASTA
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format.
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remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta
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categories:
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- Genomic Interval Operations

‎tools/genebed_maf_to_fasta/genebed_maf_to_fasta.xml‎

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<tests>
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<test>
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<param name="input1" dbkey="hg38" value="maf_to_fasta-in1.bed"/>
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<param name="maf_source" value="cached"/>
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<param name="species" value="hg38,eulFla1,mm10"/>
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<conditional name="maf_source_type">
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<param name="maf_source" value="cached"/>
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<param name="species" value="hg38,eulFla1,mm10"/>
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</conditional>
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<param name="overwrite_with_gaps" value="True"/>
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<output name="out_file1" file="maf_to_fasta-out1.fasta" />
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</test>
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<test>
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<param name="input1" dbkey="hg38" value="maf_to_fasta-in2.bed"/>
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<param name="maf_source" value="user"/>
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<param name="maf_file" dbkey="hg38" value="maf_to_fasta-in2.maf"/>
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<param name="species" value="hg38,eulFla1,mm10"/>
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<conditional name="maf_source_type">
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<param name="maf_source" value="user"/>
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<param name="maf_file" dbkey="hg38" value="maf_to_fasta-in2.maf"/>
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<param name="species" value="hg38,eulFla1,mm10"/>
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</conditional>
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<param name="overwrite_with_gaps" value="True"/>
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<output name="out_file1" file="maf_to_fasta-out2.fasta" />
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</test>

‎tools/interval2maf/.shed.yml‎

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owner: iuc
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description: Extract MAF blocks given a set of intervals
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homepage_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf/
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long_description: |
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This tool takes genomic coordinates, superimposes them on multiple alignments
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(in MAF format), and excises alignment blocks corresponding to each set of
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coordinates.
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remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf
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categories:
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- Genomic Interval Operations

‎tools/interval2maf/interval2maf.xml‎

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<tests>
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<test>
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<param name="input1" dbkey="hg38" value="interval2maf-in.bed" />
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<param name="maf_source" value="user" />
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<param name="mafFile" dbkey="hg38" value="interval2maf-in1.maf" />
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<param name="species" value="hg38,mm10,eulFla1" />
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<param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
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<conditional name="maf_source_type">
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<param name="maf_source" value="user" />
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<param name="mafFile" dbkey="hg38" value="interval2maf-in1.maf" />
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<param name="species" value="hg38,mm10,eulFla1" />
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</conditional>
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<conditional name="split_blocks_by_species_selector">
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<param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
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</conditional>
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<output name="out_file1" file="interval2maf-out1.maf" />
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</test>
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<test>
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<param name="input1" dbkey="hg38" value="interval2maf-in.bed"/>
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<param name="maf_source" value="cached"/>
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<param name="mafType" value="TEST"/>
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<param name="species" value="hg38,mm10,eulFla1" />
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<param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
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<conditional name="maf_source_type">
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<param name="maf_source" value="cached"/>
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<param name="mafType" value="TEST"/>
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<param name="species" value="hg38,mm10,eulFla1" />
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</conditional>
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<conditional name="split_blocks_by_species_selector">
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<param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
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</conditional>
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<output name="out_file1" file="interval2maf-out2.maf" />
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</test>
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<test>
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<param name="input1" dbkey="hg38" value="interval2maf-in.bed"/>
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<param name="maf_source" value="cached"/>
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<param name="mafType" value="TEST"/>
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<param name="species" value="hg38,mm10,eulFla1" />
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<param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
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<conditional name="maf_source_type">
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<param name="maf_source" value="cached"/>
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<param name="mafType" value="TEST"/>
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<param name="species" value="hg38,mm10,eulFla1" />
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</conditional>
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<conditional name="split_blocks_by_species_selector">
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<param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
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</conditional>
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<output name="out_file1" file="interval2maf-out3.maf" />
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</test>
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</tests>

‎tools/parse_mito_blast/.shed.yml‎

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owner: iuc
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description: Filtering blast out from querying assembly against mitochondrial database.
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homepage_url: https://github.com/VGP/vgp-assembly/tree/master/galaxy_tools/parse_mito_blast
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long description: |
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long_description: |
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This tool is intended for use on the tabular (format 6) output generated by blastn. Depending on filtering choices, blast will output \
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all the alignments it generates. Often there are multiple overlapping alignments for a unique query sequence-accession number pair. This tool \
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collects all alignments between a given pair and calculates the total coverage between the query and accession number, taking into /
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account overlapping alignments. Therefore a user can figure out how much of their query sequence actually identifies with a subject /
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sequence (acc #). This tool was designed for use in the VGP decontamination pipeline - in particular for deciding whether a scaffold /
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(sequence) is of mitochondrial origin. Parse_mito_blast generates a synthesized, tabular report of coverage for scaffolds with >95% /
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identity to a mitochondrial subject sequence.
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remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast
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categories:
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- Sequence Analysis

‎tools/plasmidfinder/.shed.yml‎

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description: Plasmid identification in bacteria
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name: "plasmidfinder"
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owner: "iuc"
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long_description: |

‎tools/plasmidfinder/plasmidfinder.xml‎

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<test expect_num_outputs="6">
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<section name="input">
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<param name="input_file" value="contigs.fasta"/>
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<param name="input_type" value="genome"/>
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<param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
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</section>
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<section name="output_files">
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<test expect_num_outputs="4">
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<section name="input">
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<param name="input_file" value="data.fastq.gz"/>
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<param name="input_type" value="raw"/>
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<param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
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</section>
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<section name="output_files">
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<test expect_num_outputs="3">
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<section name="input">
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<param name="input_file" value="contigs.fasta"/>
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<param name="input_type" value="genome"/>
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<param name="database_name" value="plasmidfinder_9002e7282dd0_2022-12-20"/>
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</section>
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<section name="options">
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<help><![CDATA[
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**What it does**
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PlasmidFinder characterize plasmid sequences into whole genome sequencing.
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It is based on the [plasmidfinder database](https://bitbucket.org/genomicepidemiology/plasmidfinder_db/) with hundreds sequences.
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It is based on the [plasmidfinder database](https://bitbucket.org/genomicepidemiology/plasmidfinder_db) with hundreds sequences.
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**Input**
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PlasmidFinder takes raw data (with a k-mer analysisi) as reads or genome assembly (blastn analysis) to search plasmids.
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**Output**

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