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blastn.xml
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<tool id="blastn" name="Identify reads with blastn and find taxonomy">
<!-- description>blastn wrapper and taxonomy finder</description-->
<requirements>
<requirement type="package" version="3.8.2">python</requirement>
<requirement type="package" version="1.76">biopython</requirement>
<requirement type="package" version="2.13.0">blast</requirement>
</requirements>
<command>
<![CDATA[
bash '$__tool_directory__/blastn.sh'
$input_type.type
$input_type.input
$database_type.database
$task
$max_target_seqs
$output_format.output_format_type
$log_output
#if $input_type.type == "fasta"
$blast_output_fasta
#elif $input_type.type == "zip"
$blast_output_zip
#end if
#if $output_format.output_format_type == "custom_taxonomy"
$output_format.taxonomy_method
$output_format.coverage
#else
"none"
"none"
#end if
$identity
$blast_output_original
$database_type.type
]]>
</command>
<macros>
<macro name="zip_file_input_macro">
<param format="zip" name="input" type="data" label="zip file containing fasta"/>
</macro>
<macro name="fasta_file_input_macro">
<param format="fasta" name="input" type="data" label="fasta file"/>
</macro>
<macro name="taxonomy_macro">
<param name="taxonomy_method" type="select" multiple="false" label="Taxonomy source">
<option value="none">None</option>
<option value="default" selected="true">Taxonomy of the database from the hit</option>
<option value="GBIF" selected="true">GBIF or Catalogue of Life (GBIF highest priority)</option>
</param>
<param name="coverage" type="float" label="Query Coverage percentage cutoff" value="80" min="0.0" max="100"/>
</macro>
<macro name="local_databases">
<param name="database" type="select" multiple="true" label="Database">
<option value="/data/blast_databases/CO1/CO1.fa" label="genbankco1">Genbank CO1 (2022-03-16)</option>
<!-- <option value="/extend/blast_databases/BOLD/bold_all_sequences_taxonomy_species_only_nodups.fa" label="boldnodups">BOLD species only no duplicates</option>
<option value="/extend/blast_databases/genbank/nt" label="genbankfull">Genbank (2022-03-16)</option>
<option value="/extend/blast_databases/CO1/CO1.fa" label="genbankco1">Genbank CO1 (2022-03-16)</option>
<option value="/extend/blast_databases/12S/12S.fa" label="genbank12S">Genbank 12S (2022-03-16)</option>
<option value="/extend/blast_databases/16S/16S.fa" label="genbank16S">Genbank 16S (2022-03-16)</option>
<option value="/extend/blast_databases/18S/18S.fa" label="genbank18S">Genbank 18S (2022-03-16)</option>
<option value="/extend/blast_databases/ITS/ITS.fa" label="genbankits">Genbank ITS (2022-03-16)</option>
<option value="/extend/blast_databases/matK/matK.fa" label="genbankmatk">Genbank matK (2022-03-16)</option>
<option value="/extend/blast_databases/rbcL/rbcL.fa" label="genbankrbcl">Genbank rbcL (2022-03-16)</option>
<option value="/extend/blast_databases/trnl/trnl.fa" label="genbanktrnl">Genbank trnl (2022-03-16)</option>
<option value="/extend/blast_databases/bacterial_genome_selection/bacterial_genome_selection.fa" label="genbankbacterialgenome">Genbank bacterial genome selection (2022-03-16)</option>
<option value="/extend/blast_databases/UNITE/UNITE.fa" label="unite">UNITE</option>
<option value="/extend/blast_databases/SILVA/SILVA_138_SSUParc_tax_silva_taxonomy.fasta" label="silva">SILVA 138.1 SSUParc</option>
<option value="/extend/blast_databases/waterscan/waterscan.fa" label="waterscan">waterscan</option>
<option value="/extend/blast_databases/waterscan/filtered_waterscan.fa" label="waterscan_filter">waterscan filtered</option>
<option value="/extend/blast_databases/waterscan/klassev2.fa" label="klasse">Klasse</option> -->
</param>
</macro>
<macro name="user_input_fasta">
<param format="fasta" name="database" type="data" label="fasta file"/>
</macro>
</macros>
<inputs>
<conditional name="input_type">
<param name="type" type="select" multiple="false" label="Input type">
<option value="zip">zip</option>
<option value="fasta" selected="true">fasta</option>
</param>
<when value="zip">
<expand macro="zip_file_input_macro"/>
</when>
<when value="fasta">
<expand macro="fasta_file_input_macro"/>
</when>
</conditional>
<conditional name="database_type">
<param name="type" type="select" multiple="false" label="Subject database/sequences">
<option value="local" selected="true">Locally installed BLAST database</option>
<option value="user">FASTA file from your history</option>
</param>
<when value="local">
<expand macro="local_databases"/>
</when>
<when value="user">
<expand macro="user_input_fasta"/>
</when>
</conditional>
<!--<param name="taxidlist" type="select" multiple="false" label="NCBI taxonomy filter" dynamic_options="taxon_filter(database)"/>-->
<param name="task" type="select" multiple="false" label="Task">
<option value="blastn">blastn</option>
<option value="megablast" selected="true">megablast</option>
</param>
<conditional name="output_format">
<param name="output_format_type" type="select" multiple="false" label="Output format">
<option value="custom_taxonomy" selected="true">With taxonomy (Default)</option>
<option value="0">Pairwise (can be used with MEGAN)</option>
<option value="6">Tabular</option>
<option value="8">Text ASN.1</option>
<option value="11">BLAST archive format (ASN.1)</option>
</param>
<when value="custom_taxonomy">
<expand macro="taxonomy_macro"/>
</when>
</conditional>
<param name="identity" type="float" label="Identity percentage cutoff" value="97" min="0.0" max="100"/>
<param name="max_target_seqs" type="integer" label="Maximum number of BLAST hits per sequence" value="1" min="1"/>
</inputs>
<!--<code file="/home/ubuntu/testmapMarten/test/Marten/github_scripts/galaxy-tool-BLAST/test_tool_form_utils.py"/>-->
<outputs>
<data format="txt" type="data" name="log_output" label="$input_type.input.display_name log"/>
<!--<data format="tabular" type="data" name="blast_output" label="$input_type.input.display_name BLAST" />-->
<data format="zip" type="data" name="blast_output_zip" label="$input_type.input.display_name BLAST">
<filter>input_type['type'] != "fasta"</filter>
</data>
<!-- Output with original taxonomy -->
<data format="tabular" type="data" name="blast_output_original" label="$input_type.input.display_name BLAST gbif taxonomy">
<filter>input_type['type'] == "fasta"</filter>
<filter>output_format['taxonomy_method'] == "GBIF"</filter>
</data>
<data format="tabular" type="data" name="blast_output_fasta" label="$input_type.input.display_name BLAST original taxonomy">
<filter>input_type['type'] == "fasta"</filter>
<change_format>
<when input="output_format.output_format_type" value="custom_taxonomy" format="tabular"/>
<when input="output_format.output_format_type" value="6" format="tabular"/>
<when input="output_format.output_format_type" value="8" format="txt"/>
<when input="output_format.output_format_type" value="0" format="txt"/>
<when input="output_format.output_format_type" value="11" format="txt"/>
</change_format>
</data>
</outputs>
<tests>
<test>
<param name="test_input" value="test_input.txt"/>
<output name="test_outout" file="test_output.txt"/>
</test>
</tests>
<help>
</help>
</tool>