Mercurial > repos > bgruening > sylph_query
diff macros.xml @ 0:d2a4c2cb8779 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/main/tools/sylph commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
| author | bgruening |
|---|---|
| date | Fri, 23 May 2025 09:49:04 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri May 23 09:49:04 2025 +0000 @@ -0,0 +1,216 @@ +<macros> + <token name="@TOOL_VERSION@">0.8.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@LICENSE@">MIT</token> + <token name="@DB_SELECTOR@"><![CDATA[ + #if $database_select.select == 'cached' or $database_select.select == 'cached_and_custom': + #set $databases = str($database_select.sylph_database.fields.path).split(',') + #for $number, $current_db in enumerate($databases): + #set $db_name = str($number) + "_sylph_database.syldb" + ln -s '$current_db' '$db_name' && + #end for + #end if + + #if $database_select.select == 'cached' + #set $metadata = str($database_select.sylph_database.fields.sylph_tax_identifier).split(',') + #set metadata_files = '' + #for $number, $current_metadata in enumerate($metadata): + #set metadata_files = str($metadata_files) + str($current_metadata) + ' ' + #end for + #end if + + ]]></token> + <token name="@SINGLE_INPUT_FASTQ@"><![CDATA[ + #if $sketch_reads.input.ext == 'fastqsanger' + #set $ext = 'fastq' + #else if $sketch_reads.input.ext == 'fastqsanger.gz': + #set $ext = 'fastq.gz' + #else: + #set $ext = str($sketch_reads.input.ext) + #end if + #if $sketch_reads.input.element_identifier.endswith('.fastq') or $sketch_reads.input.element_identifier.endswith('.fastq.gz'): + #set $input = re.sub(r'\s+', '_', $sketch_reads.input.element_identifier) + #else: + #set $input = re.sub(r'\s+', '_', $sketch_reads.input.element_identifier + '.' + str($ext)) + #end if + ln -s '$sketch_reads.input' '$input' && + ]]></token> + <token name="@SINGLE_GROUP_FASTQ@"><![CDATA[ + #set input = '' + #for $number, $current_file in enumerate($sketch_reads.input): + #if $current_file.ext == 'fastqsanger' + #set $ext = 'fastq' + #else if $current_file.ext == 'fastqsanger.gz': + #set $ext = 'fastq.gz' + #else: + #set $ext = str($current_file.ext) + #end if + #if $current_file.element_identifier.endswith('.fastq') or $current_file.element_identifier.endswith('.fastq.gz'): + #set $current_input = re.sub(r'\s+', '_', $current_file.element_identifier) + #else: + #set $current_input = re.sub(r'\s+', '_', $current_file.element_identifier + '.' + str($ext)) + #end if + ln -s '${current_file}' '$current_input' && + #set input = str($input) + ' ' + str($current_input) + #end for + ]]></token> + <token name="@PAIRED@"><![CDATA[ + #if $sketch_reads.input_1.ext == 'fastqsanger' + #set $ext_1 = 'fastq' + #else if $sketch_reads.input_1.ext == 'fastqsanger.gz': + #set $ext_1 = 'fastq.gz' + #else: + #set $ext_1 = str($sketch_reads.input_1.ext) + #end if + + #if $sketch_reads.input_2.ext == 'fastqsanger' + #set $ext_2 = 'fastq' + #else if $sketch_reads.input_2.ext == 'fastqsanger.gz': + #set $ext_2 = 'fastq.gz' + #else: + #set $ext_2 = str($sketch_reads.input_2.ext) + #end if + + #if $sketch_reads.input_1.element_identifier.endswith('.fastq') or $sketch_reads.input_1.element_identifier.endswith('.fastq.gz'): + #set $read1 = re.sub(r'\s+', '_', $sketch_reads.input_1.element_identifier) + #else: + #set $read1 = re.sub(r'\s+', '_', str($sketch_reads.input_1.element_identifier) + '.' + str($ext_1)) + #end if + #if $sketch_reads.input_2.element_identifier.endswith('.fastq') or $sketch_reads.input_2.element_identifier.endswith('.fastq.gz'): + #set $read2 = re.sub(r'\s+', '_', $sketch_reads.input_2.element_identifier) + #else: + #set $read2 = re.sub(r'\s+', '_', str($sketch_reads.input_2.element_identifier) + '.' + str($ext_2)) + #end if + ln -s '$sketch_reads.input_1' '$read1' && + ln -s '$sketch_reads.input_2' '$read2' && + ]]></token> + <token name="@PAIRED_GROUP@"><![CDATA[ + #if $sketch_reads.input.forward.ext == 'fastqsanger' + #set $ext_1 = 'fastq' + #else if $sketch_reads.input.forward.ext == 'fastqsanger.gz': + #set $ext_1 = 'fastq.gz' + #else: + #set $ext_1 = str($sketch_reads.input.forward.ext) + #end if + + #if $sketch_reads.input.reverse.ext == 'fastqsanger' + #set $ext_2 = 'fastq' + #else if $sketch_reads.input.reverse.ext == 'fastqsanger.gz': + #set $ext_2 = 'fastq.gz' + #else: + #set $ext_2 = str($sketch_reads.input.reverse.ext) + #end if + + #set $read1 = re.sub(r'\s+', '_', str($sketch_reads.input.element_identifier) + '.' + str($ext_1)) + #set $read2 = re.sub(r'\s+', '_', str($sketch_reads.input.element_identifier) + '_r2.' + str($ext_2)) + ln -s '$sketch_reads.input.forward' '$read1' && + ln -s '$sketch_reads.input.reverse' '$read2' && + ]]></token> + <token name="@SINGLE_INPUT_FASTA@"><![CDATA[ + #if $sketch_fasta.input.ext == 'fasta' + #set $ext = 'fasta' + #else if $sketch_fasta.input.ext == 'fasta.gz': + #set $ext = 'fasta.gz' + #else: + #set $ext = str($sketch_fasta.input.ext) + #end if + #if $sketch_fasta.input.element_identifier.endswith('.fasta') or $sketch_fasta.input.element_identifier.endswith('.fasta.gz'): + #set $input = re.sub(r'\s+', '_', $sketch_fasta.input.element_identifier) + #else: + #set $input = re.sub(r'\s+', '_', $sketch_fasta.input.element_identifier + '.' + str($ext)) + #end if + ln -s '$sketch_fasta.input' '$input' && + ]]></token> + <token name="@SINGLE_GROUP_FASTA@"><![CDATA[ + #set input = '' + #for $number, $current_file in enumerate($sketch_fasta.input): + #if $sketch_fasta.input.ext == 'fasta' + #set $ext = 'fasta' + #else if $sketch_fasta.input.ext == 'fasta.gz': + #set $ext = 'fasta.gz' + #else: + #set $ext = str($current_file.ext) + #end if + #if $current_file.element_identifier.endswith('.fasta') or $current_file.element_identifier.endswith('.fasta.gz'): + #set $current_input = re.sub(r'\s+', '_', $current_file.element_identifier) + #else: + #set $current_input = re.sub(r'\s+', '_', $current_file.element_identifier + '.' + str($ext)) + #end if + ln -s '${current_file}' '$current_input' && + #set input = str($input) + ' ' + str($current_input) + #end for + ]]></token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">sylph</requirement> + <requirement type="package" version="3.11">python</requirement> + <requirement type="package" version="2.2">pandas</requirement> + <yield /> + </requirements> + </xml> + <xml name="citation"> + <citations> + <citation type="doi">10.1038/s41587-024-02412-y</citation> + </citations> + </xml> + <xml name="creator"> + <creator> + <person givenName="Tyler" familyName="Collins"/> + <person givenName="Alexander" familyName="Ostrovsky"/> + <person givenName="Hugo" familyName="Lefeuvre"/> + </creator> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">sylph</xref> + </xrefs> + </xml> + <xml name="input_database"> + <when value="custom"> + <conditional name="sketch_fasta"> + <param name="type_fasta" type="select" label="Select the type of fasta used"> + <option value="single_fasta">Individual fasta files</option> + <option value="single_group_fasta">Group of fasta files</option> + </param> + <when value="single_fasta"> + <param name="input" type="data" format="fasta,fasta.gz" label="Fasta files"/> + </when> + <when value="single_group_fasta"> + <param name="input" type="data" format="fasta,fasta.gz" label="Fasta files" multiple="true"/> + </when> + </conditional> + <param name="compression" type="integer" min="0" value="200" label="Compression" help="Memory/runtime scale like 1/c; higher c is faster but less sensitive at low coverage. The -c for genomes must be than >= the -c for reads (strict > is allowed) (-c)" /> + <param name="grouped_genomes" type="boolean" checked="false" label="Creating a database of contigs or if genomes are all in one fasta file" truevalue="Yes" falsevalue="No" help="Considers every record in a fasta (i.e. contig) as a genome (-i)" /> + </when> + <when value="cached_and_custom"> + <param label="Select a sylph database" name="sylph_database" type="select" multiple="true" optional="false"> + <options from_data_table="sylph_databases"> + <filter type="static_value" value="1" column="version"/> + <validator message="No Sylph databases are available" type="no_options" /> + </options> + </param> + <conditional name="sketch_fasta"> + <param name="type_fasta" type="select" label="Select the type of fasta used"> + <option value="single_fasta">Individual fasta files</option> + <option value="single_group_fasta">Group of fasta files</option> + </param> + <when value="single_fasta"> + <param name="input" type="data" format="fasta,fasta.gz" label="Fasta files"/> + </when> + <when value="single_group_fasta"> + <param name="input" type="data" format="fasta,fasta.gz" label="Fasta files" multiple="true"/> + </when> + </conditional> + <param name="compression" type="integer" min="0" value="200" label="Compression" help="Memory/runtime scale like 1/c; higher c is faster but less sensitive at low coverage. The -c for genomes must be than >= the -c for reads (strict > is allowed) (-c)" /> + <param name="grouped_genomes" type="boolean" checked="false" label="Creating a database of contigs or if genomes are all in one fasta file" truevalue="Yes" falsevalue="No" help="Considers every record in a fasta (i.e. contig) as a genome (-i)" /> + </when> + </xml> + <xml name="element_assert" token_name="" token_text=""> + <element name="@NAME@"> + <assert_contents> + <has_text text="@TEXT@"/> + <yield/> + </assert_contents> + </element> + </xml> +</macros> \ No newline at end of file