Mercurial > repos > iuc > coverm_contig
comparison macros.xml @ 3:c2a5823e4763 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982
| author | iuc |
|---|---|
| date | Wed, 26 Jul 2023 07:35:24 +0000 |
| parents | 688a777e1b19 |
| children | 1dcea261abbe |
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| 2:f8cb3f0a19fa | 3:c2a5823e4763 |
|---|---|
| 1 <macros> | 1 <macros> |
| 2 <token name="@TOOL_VERSION@">0.6.1</token> | |
| 3 <token name="@VERSION_SUFFIX@">1</token> | |
| 4 <token name="@PROFILE@">22.01</token> | |
| 2 <xml name="requirements"> | 5 <xml name="requirements"> |
| 3 <requirements> | 6 <requirements> |
| 4 <requirement type="package" version="@TOOL_VERSION@">coverm</requirement> | 7 <requirement type="package" version="@TOOL_VERSION@">coverm</requirement> |
| 5 </requirements> | 8 </requirements> |
| 6 </xml> | 9 </xml> |
| 7 <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token> | 10 <xml name="bio_tools"> |
| 8 <token name="@TOOL_VERSION@">0.6.1</token> | 11 <xrefs> |
| 9 <token name="@VERSION_SUFFIX@">0</token> | 12 <xref type="bio.tools">coverm</xref> |
| 10 <token name="@PROFILE@">22.01</token> | 13 </xrefs> |
| 14 </xml> | |
| 11 <xml name="citation"> | 15 <xml name="citation"> |
| 12 <citations> | 16 <citations> |
| 13 <citation type="bibtex"> | 17 <citation type="bibtex"> |
| 14 @misc{githubCoverm, | 18 @misc{githubCoverm, |
| 15 author = {B J. Woodcroft}, | 19 author = {B J. Woodcroft}, |
| 20 url = {https://github.com/wwood/CoverM} | 24 url = {https://github.com/wwood/CoverM} |
| 21 } | 25 } |
| 22 </citation> | 26 </citation> |
| 23 </citations> | 27 </citations> |
| 24 </xml> | 28 </xml> |
| 25 <xml name="genome_opt"> | 29 <xml name="mapped"> |
| 26 <conditional name="genome"> | 30 <param name="mapped" type="select" label="Have the reads already been mapped to contigs?"> |
| 27 <param name="ref_or_genome" type="select" label="Select if you want to specify additional genome files."> | 31 <option value="mapped">Yes (no read mapping algorithm will be undertaken)</option> |
| 28 <option value="genomic">yes</option> | 32 <option value="not-mapped" selected="true">No</option> |
| 29 <option value="none" selected="true">No (Only when BAM files are provided)</option> | 33 </param> |
| 34 </xml> | |
| 35 <xml name="assembly_mode"> | |
| 36 <param name="mode" type="select" label="Assembly mode?" help="Useful to know if contigs have been generated all samples together (co-assembly) or on each sample individually (individual assembly)"> | |
| 37 <option value="individual">Individual assembly (1 contig file per sample)</option> | |
| 38 <option value="co" selected="true">Co-assembly (1 contig file for several samples)</option> | |
| 39 </param> | |
| 40 </xml> | |
| 41 <xml name="mapped_params"> | |
| 42 <conditional name="mode"> | |
| 43 <expand macro="assembly_mode"/> | |
| 44 <when value="individual"> | |
| 45 <param argument="--bam-files" type="data" format="bam" label="BAM file(s)" help="These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n)."/> | |
| 46 </when> | |
| 47 <when value="co"> | |
| 48 <param argument="--bam-files" type="data" format="bam" multiple="true" label="BAM file(s)" help="These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n)."/> | |
| 49 </when> | |
| 50 </conditional> | |
| 51 <param argument="--sharded" type="boolean" truevalue="--sharded" falsevalue="" checked="false" label="BAM file(s) read-sorted alignments of a set of reads mapped to multiple reference contig sets?" help="If set, it will choose the best hit for each read pair" /> | |
| 52 </xml> | |
| 53 <token name="@BAMS@"><![CDATA[ | |
| 54 #if $mapped.mode.mode == 'individual' | |
| 55 #set $fn = 'bam/' + re.sub('[^\s\w\-\\.]', '_', str($mapped.mode.bam_files.element_identifier)) | |
| 56 #silent $bam_fp.append( $fn ) | |
| 57 ln -s '$mapped.mode.bam_files' '$fn' && | |
| 58 #else | |
| 59 #for $i, $bam in enumerate($mapped.mode.bam_files) | |
| 60 #set $fn = 'bam/' + re.sub('[^\s\w\-\\.]', '_', str($bam.element_identifier)) + '_' + str($i) | |
| 61 #silent $bam_fp.append( $fn ) | |
| 62 ln -s '$bam' '$fn' && | |
| 63 #end for | |
| 64 #end if | |
| 65 ]]></token> | |
| 66 <xml name="genomic"> | |
| 67 <conditional name="genomic"> | |
| 68 <param type="select" name="source" label="Source of FASTA files with each genome" > | |
| 69 <option value="history" selected="true">History</option> | |
| 70 <option value="builtin">Built-in</option> | |
| 30 </param> | 71 </param> |
| 31 <when value="none"> | 72 <when value="history"> |
| 32 <param argument="--single-genome" type="boolean" truevalue="--single-genome" falsevalue="" checked="false" label="All contigs are from the same genome."/> | 73 <param argument="--genome-fasta-files" type="data" format="fasta" multiple="true" label="FASTA files of each genome"/> |
| 33 <param type="text" name="separator" optional="true" label="Character, that separates genome names from contig names in the reference file." > | 74 </when> |
| 34 <sanitizer> | 75 <when value="builtin"> |
| 35 <valid initial="string.punctuation"> | 76 <param argument="--genome-fasta-files" type="select" multiple="true" label="Reference genome(s)"> |
| 36 </valid> | 77 <options from_data_table="all_fasta" /> |
| 37 </sanitizer> | |
| 38 </param> | 78 </param> |
| 39 </when> | 79 </when> |
| 40 <when value="genomic"> | 80 </conditional> |
| 41 <conditional name="genomic"> | 81 </xml> |
| 42 <param type="select" label="Reference genome source" name="source"> | 82 <xml name="cond_single_genome"> |
| 43 <option value="history" selected="true">History</option> | 83 <conditional name="cond_single_genome"> |
| 44 <option value="builtin">Built-in</option> | 84 <param argument="--single-genome" type="select" label="Are all contigs from the same genome?"> |
| 85 <option value="--single-genome">True</option> | |
| 86 <option value="">False</option> | |
| 87 </param> | |
| 88 <when value="--single-genome"/> | |
| 89 <when value=""> | |
| 90 <conditional name="genome_contig_definition"> | |
| 91 <param argument="choice" type="select" label="How to get genome names and contig names?"> | |
| 92 <option value="default" selected="true">Using default behavior</option> | |
| 93 <option value="genome-definition">Providing a file containing newline-separated list of genome name and contig</option> | |
| 94 <option value="separator">Providing character that separates genome names from contig names in the reference file</option> | |
| 45 </param> | 95 </param> |
| 46 <when value="history"> | 96 <when value="default"/> |
| 47 <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" /> | 97 <when value="genome-definition"> |
| 98 <param argument="--genome-definition" type="data" format="tabular" label="File containing newline-separated list of genome_name and contig, separated by tab, to define the genome of each contig." /> | |
| 48 </when> | 99 </when> |
| 49 <when value="builtin"> | 100 <when value="separator"> |
| 50 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)"> | 101 <param argument="--separator" type="text" label="Character that separates genome names from contig names in the reference file." > |
| 51 <options from_data_table="all_fasta" /> | |
| 52 </param> | |
| 53 </when> | |
| 54 </conditional> | |
| 55 </when> | |
| 56 </conditional> | |
| 57 </xml> | |
| 58 <xml name="genome"> | |
| 59 <conditional name="genome"> | |
| 60 <param name="ref_or_genome" type="select" label="Reference sequence mode" help="Select if you want to specify genome file(s) or a FASTA reference file or both. NOTE: If genomic FASTA files are specified, then reference is not needed as a reference FASTA file can be derived by concatenating input genomes. However, while not necessary, reference can be specified if an alternate reference sequence set is desired."> | |
| 61 <option value="genomic" selected="true">Reference genome</option> | |
| 62 <option value="reference">Contigs (e.g. concatenated genomes or metagenome assembly)</option> | |
| 63 </param> | |
| 64 <when value="genomic"> | |
| 65 <conditional name="genomic"> | |
| 66 <param type="select" label="Reference genome source" name="source"> | |
| 67 <option value="history" selected="true">History</option> | |
| 68 <option value="builtin">Built-in</option> | |
| 69 </param> | |
| 70 <when value="history"> | |
| 71 <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" /> | |
| 72 </when> | |
| 73 <when value="builtin"> | |
| 74 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)"> | |
| 75 <options from_data_table="all_fasta" /> | |
| 76 </param> | |
| 77 </when> | |
| 78 </conditional> | |
| 79 </when> | |
| 80 <when value="reference"> | |
| 81 <param type="data" name="ref_source" multiple="true" label="Contigs file(s)" format="fasta" help="If multiple references FASTA files are provided and 'sharded' is specified, then reads will be mapped to references separately as sharded BAMs."/> | |
| 82 <conditional name="cond_single_genome"> | |
| 83 <param name="single_genome" type="select" label="All contigs are from a single genome"> | |
| 84 <option value="--single-genome">True</option> | |
| 85 <option value="false">False</option> | |
| 86 </param> | |
| 87 <when value="--single-genome"> | |
| 88 <param type="data" name="genome_definition" format="tsv" optional="true" label="File containing newline-separated list of genome_name and contig, separated by tab, to define the genome of each contig." /> | |
| 89 </when> | |
| 90 <when value="false"> | |
| 91 <param type="text" argument="--separator" optional="true" label="Character, that separates genome names from contig names in the reference file." > | |
| 92 <sanitizer> | 102 <sanitizer> |
| 93 <valid initial="string.punctuation"> | 103 <valid initial="string.punctuation"> |
| 94 </valid> | 104 </valid> |
| 95 </sanitizer> | 105 </sanitizer> |
| 96 </param> | 106 </param> |
| 97 </when> | 107 </when> |
| 98 </conditional> | |
| 99 <conditional name="add_genome"> | |
| 100 <param name="add_genome" type="select" label="Add additional Genome Files"> | |
| 101 <option value="true">Yes</option> | |
| 102 <option value="false" selected="true">No</option> | |
| 103 </param> | |
| 104 <when value="true"> | |
| 105 <conditional name="add_genomic"> | |
| 106 <param type="select" label="Reference genome source" name="source"> | |
| 107 <option value="history" selected="true">History</option> | |
| 108 <option value="builtin">Built-in</option> | |
| 109 </param> | |
| 110 <when value="history"> | |
| 111 <param type="data" name="fasta_history" multiple="true" label="Single FASTA file of contigs" format="fasta" /> | |
| 112 </when> | |
| 113 <when value="builtin"> | |
| 114 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome"> | |
| 115 <options from_data_table="all_fasta" /> | |
| 116 </param> | |
| 117 </when> | |
| 118 </conditional> | |
| 119 </when> | |
| 120 <when value="false"> | |
| 121 </when> | |
| 122 </conditional> | 108 </conditional> |
| 123 </when> | 109 </when> |
| 124 </conditional> | 110 </conditional> |
| 125 </xml> | 111 </xml> |
| 126 <xml name="reads_for_contig"> | 112 <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token> |
| 127 <conditional name="reads"> | 113 <xml name="read_type"> |
| 128 <param type="select" label="Read type" name="read_type"> | 114 <param name="type" type="select" label="Read type" > |
| 129 <option value="paired">Paired end</option> | 115 <option value="single">Single end</option> |
| 130 <option value="paired_collection" selected="true">Paired collection</option> | 116 <option value="paired">Paired end</option> |
| 131 <option value="single">Single ended</option> | 117 <option value="paired_collection" selected="true">Paired collection</option> |
| 132 <option value="interleaved">Interleaved</option> | 118 <option value="interleaved">Interleaved</option> |
| 133 <option value="bam">BAM file(s)</option> | 119 </param> |
| 134 </param> | 120 </xml> |
| 121 <xml name="paired_reads"> | |
| 122 <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." /> | |
| 123 </xml> | |
| 124 <xml name="individual_assembly_reads"> | |
| 125 <conditional name="read_type"> | |
| 126 <expand macro="read_type"/> | |
| 127 <when value="single"> | |
| 128 <param argument="--single" type="data" format="@INPUT_FORMATS@" label="Single Read" /> | |
| 129 </when> | |
| 135 <when value="paired"> | 130 <when value="paired"> |
| 136 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" /> | 131 <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" label="Forward FASTA/Q file for mapping" /> |
| 137 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" /> | 132 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" label="Reverse FASTA/Q file for mapping" /> |
| 138 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> | |
| 139 </when> | 133 </when> |
| 140 <when value="paired_collection"> | 134 <when value="paired_collection"> |
| 141 <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order" /> | 135 <expand macro="paired_reads"/> |
| 142 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> | 136 </when> |
| 143 </when> | 137 <when value="interleaved"> |
| 138 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" label="Interleaved FASTA/Q files for mapping" /> | |
| 139 </when> | |
| 140 </conditional> | |
| 141 </xml> | |
| 142 <xml name="ref_or_genome"> | |
| 143 <param name="ref_or_genome" type="select" label="Genome definition"> | |
| 144 <option value="contigs" selected="true">From contigs (e.g. concatenated genomes or metagenome assembly)</option> | |
| 145 <option value="genomic">From FASTA files with each genome</option> | |
| 146 </param> | |
| 147 </xml> | |
| 148 <xml name="individual_assembly_reference"> | |
| 149 <param argument="--reference" type="data" format="fasta" label="Contigs"/> | |
| 150 </xml> | |
| 151 <token name="@INDIVIDUAL_ASSEMBLY_READS@"><![CDATA[ | |
| 152 #set $reads = $mapped.mode.read_type | |
| 153 #if $reads.type == 'single' | |
| 154 #set $fn = "single/" + re.sub('[^\s\w\-\\.]', '_', str($reads.single.element_identifier)) | |
| 155 #silent $single_fp.append( $fn ) | |
| 156 ln -s '$reads.single' '$single_fp' && | |
| 157 #else if $reads.type == 'paired' | |
| 158 #set $fn = "fw/" + re.sub('[^\s\w\-\\.]', '_', str($reads.read1.element_identifier)) | |
| 159 #silent $fw_fp.append( $fn ) | |
| 160 ln -s '$reads.read1' '$fn' && | |
| 161 #set $fn = "rv/" + re.sub('[^\s\w\-\\.]', '_', str($reads.read2.element_identifier)) | |
| 162 ln -s '$reads.read2' '$fn' && | |
| 163 #silent $rv_fp.append( $fn ) | |
| 164 #else if $reads.type == 'paired_collection' | |
| 165 #set $id = re.sub('[^\s\w\-\\.]', '_', str($reads.paired_reads.element_identifier)) | |
| 166 #set $fn = "fw/" + $id | |
| 167 #silent $fw_fp.append( $fn ) | |
| 168 ln -s '$reads.paired_reads.forward' '$fn' && | |
| 169 #set $fn = "rv/" + $id | |
| 170 #silent $rv_fp.append( $fn ) | |
| 171 ln -s '$mreads.paired_reads.reverse' '${fn}' && | |
| 172 #else if $reads.type == 'interleaved' | |
| 173 #set $fn = "interl/" + re.sub('[^\s\w\-\\.]', '_', str($reads.interleaved.element_identifier)) | |
| 174 #silent $interl_fp.append( $fn ) | |
| 175 ln -s '$reads.interleaved' '$fn' && | |
| 176 #end if | |
| 177 ]]></token> | |
| 178 <token name="@INDIVIDUAL_ASSEMBLY_REF@"><![CDATA[ | |
| 179 #set $fn = "ref/" + re.sub('[^\s\w\-\\.]', '_', str($ref.element_identifier)) | |
| 180 #silent $ref_fp.append( $fn ) | |
| 181 ln -s '$ref' '${fn}' && | |
| 182 ]]></token> | |
| 183 <token name="@GENOME_FOR_READS@"><![CDATA[ | |
| 184 #if $mapped.mode.genome.genomic.source == 'history' | |
| 185 #for $i, $genome in enumerate($mapped.mode.genome.genomic.genome_fasta_files) | |
| 186 #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.element_identifier)) | |
| 187 #silent $genome_fp.append( $fn ) | |
| 188 ln -s '$genome' '$fn' && | |
| 189 #end for | |
| 190 #else | |
| 191 #for $i, $genome in enumerate($mapped.mode.genome.genomic.genome_fasta_files) | |
| 192 #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.fields.path.element_identifier)) | |
| 193 #silent $genome_fp.append( $fn ) | |
| 194 ln -s '$genome' '$fn' && | |
| 195 #end for | |
| 196 #end if | |
| 197 ]]></token> | |
| 198 <xml name="co_assembly_reads"> | |
| 199 <conditional name="read_type"> | |
| 200 <expand macro="read_type"/> | |
| 144 <when value="single"> | 201 <when value="single"> |
| 145 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Single Read" /> | 202 <param argument="--single" type="data" format="@INPUT_FORMATS@" multiple="true" label="Single Read" /> |
| 146 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> | 203 </when> |
| 204 <when value="paired"> | |
| 205 <param argument="-1" name="read1" type="data" format="@INPUT_FORMATS@" multiple="true" label="Forward FASTA/Q file(s) for mapping" /> | |
| 206 <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" multiple="true" label="Reverse FASTA/Q file(s) for mapping" /> | |
| 207 </when> | |
| 208 <when value="paired_collection"> | |
| 209 <expand macro="paired_reads"/> | |
| 147 </when> | 210 </when> |
| 148 <when value="interleaved"> | 211 <when value="interleaved"> |
| 149 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" /> | 212 <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" multiple="true" label="Interleaved FASTA/Q files(s) for mapping" /> |
| 150 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> | 213 </when> |
| 151 </when> | 214 </conditional> |
| 152 <when value="bam"> | 215 </xml> |
| 153 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" help="BAM file(s). These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n). When specified, no read mapping algorithm is undertaken."/> | 216 <xml name="co_assembly_reference"> |
| 154 <param type="data" name="ref_fasta_history" optional="true" multiple="true" label="FASTA file(s) of contigs" format="fasta" /> | 217 <param argument="--reference" type="data" format="fasta" multiple="true" label="Contigs" /> |
| 155 </when> | 218 <param argument="--sharded" type="boolean" truevalue="--sharded" falsevalue="" checked="false" label="Mapping reads to references separately as sharded BAMs?" /> |
| 156 </conditional> | 219 </xml> |
| 157 </xml> | 220 <token name="@CO_ASSEMBLY_READS@"><![CDATA[ |
| 158 <xml name="reads"> | 221 #if $reads.type == 'single' |
| 159 <conditional name="reads"> | 222 #for $i, $read in enumerate($reads.single) |
| 160 <param type="select" label="Read type" name="read_type"> | 223 #set $fn = "single/" + re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier)) + "_single_" + str($i) + $extra |
| 161 <option value="single">Single ended</option> | 224 #silent $single_fp.append( $fn ) |
| 162 <option value="paired">Paired end</option> | 225 ln -s '$read' '$fn' && |
| 163 <option value="paired_collection" selected="true">Paired collection</option> | 226 #end for |
| 164 <option value="interleaved">Interleaved</option> | 227 #else if $reads.type == 'paired' |
| 165 <option value="bam">BAM file(s)</option> | 228 #for $i, $read in enumerate($reads.read1) |
| 166 </param> | 229 #set $id = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier)) |
| 167 <when value="paired"> | 230 #set $fn = "fw/" + $id + "_paired_" + str($i) + $extra |
| 168 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" /> | 231 #silent $fw_fp.append( $fn ) |
| 169 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" /> | 232 ln -s '$read' '$fn' && |
| 170 <expand macro="genome"/> | 233 #end for |
| 171 </when> | 234 #for $i, $read in enumerate($reads.read2) |
| 172 <when value="paired_collection"> | 235 #set $id = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier)) |
| 173 <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="Collection of paired-reads" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." /> | 236 #set $fn = "rv/" + $id + "_paired_" + str($i) + $extra |
| 174 <expand macro="genome"/> | 237 #silent $rv_fp.append( $fn ) |
| 175 </when> | 238 ln -s '$read' '$fn' && |
| 176 <when value="single"> | 239 #end for |
| 177 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Single Read" /> | 240 #else if $reads.type == 'paired_collection' |
| 178 <expand macro="genome"/> | 241 #for $i, $read in enumerate($reads.paired_reads) |
| 179 </when> | 242 #set $id = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier)) |
| 180 <when value="interleaved"> | 243 #set $fn = "fw/" + $id + "_paired_collection_" + str($i) + $extra |
| 181 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" /> | 244 #silent $fw_fp.append( $fn ) |
| 182 <expand macro="genome"/> | 245 ln -s '$read.forward' '$fn' && |
| 183 </when> | 246 #set $fn = "rv/" + $id + "_paired_collection_" + str($i) + $extra |
| 184 <when value="bam"> | 247 #silent $rv_fp.append( $fn ) |
| 185 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" help="BAM file(s). These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n). When specified, no read mapping algorithm is undertaken."/> | 248 ln -s '$read.reverse' '$fn' && |
| 186 <expand macro="genome_opt"/> | 249 #end for |
| 187 </when> | 250 #else if $reads.type == 'interleaved' |
| 188 </conditional> | 251 #for $i, $read in enumerate($reads.interleaved) |
| 189 </xml> | 252 #set $id = re.sub('[^\s\w\-\\.]', '_', str($read.element_identifier)) |
| 190 <xml name="add_reads"> | 253 #set $fn = "interl/" + $id + "_interleaved_" + str($i) + $extra |
| 191 <section name="add_reads" title="Add an additional read"> | 254 #silent $interl_fp.append( $fn ) |
| 192 <conditional name="extra_read"> | 255 ln -s '$read' '$fn' && |
| 193 <param type="select" label="Read type" name="read_type"> | 256 #end for |
| 194 <option value="none" selected="true">None</option> | 257 #end if |
| 195 <option value="paired">Paired end</option> | 258 ]]></token> |
| 196 <option value="paired_collection">Paired collection</option> | 259 <token name="@CO_ASSEMBLY_ALL_READS@"><![CDATA[ |
| 197 <option value="single">Single ended</option> | 260 #set $reads = $mapped.mode.read_type |
| 198 <option value="interleaved">Interleaved</option> | 261 #set $extra = '' |
| 199 <option value="bam">BAM file(s)</option> | 262 @CO_ASSEMBLY_READS@ |
| 200 </param> | 263 #for $j, $s in enumerate($mapped.mode.extra_reads) |
| 201 <when value="none"> | 264 #set $reads = $s.read_type |
| 202 </when> | 265 #set $extra = str($j) |
| 203 <when value="paired"> | 266 @CO_ASSEMBLY_READS@ |
| 204 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" /> | 267 #end for |
| 205 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" /> | 268 ]]></token> |
| 206 </when> | 269 <token name="@CO_ASSEMBLY_REF@"><![CDATA[ |
| 207 <when value="paired_collection"> | 270 #for $i, $ref in enumerate($refs) |
| 208 <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order" /> | 271 #set $fn = "ref/" + re.sub('[^\s\w\-\\.]', '_', str($ref.element_identifier)) + "_" + str($i) |
| 209 </when> | 272 #silent $ref_fp.append( $fn ) |
| 210 <when value="single"> | 273 ln -s '$ref' '${fn}' && |
| 211 <param type="data" format="@INPUT_FORMATS@" name="single" multiple="true" label="Single read" /> | 274 #end for |
| 212 </when> | 275 ]]></token> |
| 213 <when value="interleaved"> | 276 <xml name="sharded"> |
| 214 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" /> | 277 <param name="sharded" type="boolean" truevalue="--sharded" falsevalue="" checked="false" label="Input BAM files are read-sorted alignments of a set of reads mapped to multiple reference contig sets. Choose the best hit for each read pair. Otherwise if mapping was carried out: Map reads to each reference, choosing the best hit for each pair." /> |
| 215 </when> | |
| 216 <when value="bam"> | |
| 217 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" /> | |
| 218 </when> | |
| 219 </conditional> | |
| 220 </section> | |
| 221 </xml> | 278 </xml> |
| 222 <xml name="mapping"> | 279 <xml name="mapping"> |
| 223 <section name="mapping" title="Mapping options" expanded="false"> | 280 <param argument="--mapper" type="select" label="Underlying mapping software used"> |
| 224 <param argument="--mapper" optional="true" type="select" label="Mapper" help="Underlying mapping software used. Default: minimap2-sr" > | 281 <option value="minimap2-sr" selected="true">minimap2 with '-x sr' option</option> |
| 225 <option value="minimap2-sr">minimap2 with '-x sr' option</option> | 282 <option value="minimap2-ont">minimap2 with '-x map-ont' option</option> |
| 226 <option value="minimap2-ont">minimap2 with '-x map-ont' option</option> | 283 <option value="minimap2-pb">minimap2 with '-x map-pb' option</option> |
| 227 <option value="minimap2-pb">minimap2 with '-x map-pb' option</option> | 284 <option value="minimap2-no-preset">minimap2 with no '-x' option</option> |
| 228 <option value="minimap2-no-preset">minimap2 with no '-x' option</option> | 285 <option value="bwa-mem">BWA-MEM using default parameters</option> |
| 229 <option value="bwa-mem">BWA-MEM using default parameters</option> | 286 </param> |
| 230 </param> | 287 </xml> |
| 231 <param argument="--min_read-aligned-length" type="integer" min="0" value="0" | 288 <xml name="alignment"> |
| 232 label="Min read aligned length" help="Exclude reads with smaller numbers of aligned bases. Default: 0" /> | 289 <section name="alignment" title="Alignment thresholding" expanded="false"> |
| 233 <param argument="--min_read-percent-identity" type="float" min="0" max="100" value="0" | 290 <param argument="--min-read-aligned-length" type="integer" min="0" value="0" |
| 234 label="Min read percent identity" help="Exclude reads by overall percent identity e.g. 95 for 95%. Default: 0" /> | 291 label="Minimum number of aligned bases" help="Reads with smaller numbers of aligned bases will be excluded" /> |
| 235 <param argument="--min_read-aligned-percent" type="float" min="0" max="100" value="0" | 292 <param argument="--min-read-percent-identity" type="float" min="0" max="100" value="0" |
| 236 label="Min read aligned percentage" help="Exclude reads by percent aligned bases e.g. 95 means 95% | 293 label="Minimum overall percent identity" help="Reads with lower overall percent identity will be excluded." /> |
| 237 of the read's bases must be aligned. Default: 0" /> | 294 <param argument="--min-read-aligned-percent" type="float" min="0" max="100" value="0" |
| 238 <param argument="--min_read-aligned-length-pair" type="integer" min="0" value="0" | 295 label="Minimum aligned base percent" help="Reads with lower percent aligned bases will be excluded" /> |
| 239 label="Min read aligned length pair" help="Exclude pairs with smaller numbers of aligned bases. | 296 <conditional name="proper_pairs_only"> |
| 240 Implies --proper-pairs-only. Default: 0" /> | 297 <param argument="--proper-pairs-only" type="select" label="Require reads to be mapped as proper pairs?"> |
| 241 <param argument="--min_read-percent-identity-pair" type="float" min="0" max="100" value="0" | 298 <option value="--proper-pairs-only">Yes</option> |
| 242 label="Min read percent identity pair" help="Exclude pairs by overall percent identity e.g. 95 for 95%. | |
| 243 Implies --proper-pairs-only. Default: 0" /> | |
| 244 <param argument="--min_read-aligned-percent-pair" type="float" min="0" max="100" value="0" | |
| 245 label="Min read aligned percentage pair" help="Exclude reads by percent aligned bases e.g. 95 means 95% of | |
| 246 the read's bases must be aligned. Implies --proper-pairs-only. Default: 0" /> | |
| 247 <param argument="--proper-pairs-only" type="boolean" truevalue="--proper-pairs-only" falsevalue="" | |
| 248 label="Require reads to be mapped as proper pairs" help="Default: not set"/> | |
| 249 <param argument="--exclude-supplementary" type="boolean" truevalue="--exclude-supplementary" falsevalue="" | |
| 250 label="Exclude supplementary alignments" help="Default: not set"/> | |
| 251 </section> | |
| 252 </xml> | |
| 253 <xml name="coverage"> | |
| 254 <section name="cov" title="Coverage calculation options" expanded="false"> | |
| 255 <param name="relative_abundance" type="boolean" falsevalue="" truevalue="relative_abundance" label="Relative abundance (default)"/> | |
| 256 <param name="mean" type="boolean" falsevalue="" truevalue="mean" label="Mean"/> | |
| 257 <conditional name="cond_methods"> | |
| 258 <param name="trimmed_mean" type="select" label="Trimmed mean"> | |
| 259 <option value="trimmed_mean">Yes</option> | |
| 260 <option value="" selected="true">No</option> | 299 <option value="" selected="true">No</option> |
| 261 </param> | 300 </param> |
| 262 <when value="trimmed_mean"> | 301 <when value="--proper-pairs-only"> |
| 263 <param name="trim_min" type="integer" min="0" value="5" label="Trim min" help="Remove this smallest fraction of positions when calculating trimmed_mean default: 5"/> | 302 <param argument="--min_read-aligned-length-pair" type="integer" min="0" value="0" |
| 264 <param name="trim_max" type="integer" min="0" value="95" label="Trim max" help="Maximum fraction for trimmed_mean calculations default: 95"/> | 303 label="Minimum number of aligned bases for pairs" help="Pairs with smaller numbers of aligned bases will be excluded." /> |
| 304 <param argument="--min-read-percent-identity-pair" type="float" min="0" max="100" value="0" | |
| 305 label="Minimum overall percent identity pair for pairs" help="Pairs by lower overall percent identity will be excluded" /> | |
| 306 <param argument="--min-read-aligned-percent-pair" type="float" min="0" max="100" value="0" | |
| 307 label="Minimum percent of read aligned bases for pair" help="Pairs with lower reads percent aligned bases will be excluded" /> | |
| 265 </when> | 308 </when> |
| 266 <when value=""/> | 309 <when value=""/> |
| 267 </conditional> | 310 </conditional> |
| 268 <param name="covered_bases" type="boolean" falsevalue="" truevalue="covered_bases" label="Covered bases"/> | 311 <param argument="--exclude-supplementary" type="boolean" truevalue="--exclude-supplementary" falsevalue="" checked="false" |
| 269 <param name="covered_fraction" type="boolean" falsevalue="" truevalue="covered_fraction" label="Covered fraction"/> | 312 label="Exclude supplementary alignments"/> |
| 270 <param name="variance" type="boolean" falsevalue="" truevalue="variance" label="Variance"/> | |
| 271 <param name="length" type="boolean" falsevalue="" truevalue="length" label="Length"/> | |
| 272 <param name="count" type="boolean" falsevalue="" truevalue="count" label="Count"/> | |
| 273 <param name="metabat" type="boolean" falsevalue="" truevalue="metabat" label="MetaBAT"/> | |
| 274 <param name="coverage_histogram" type="boolean" falsevalue="" truevalue="coverage_histogram" label="Coverage histogram"/> | |
| 275 <param name="reads_per_base" type="boolean" falsevalue="" truevalue="reads_per_base" label="Reads per base"/> | |
| 276 <param name="rpkm" type="boolean" falsevalue="" truevalue="rpkm" label="RPKM"/> | |
| 277 <param name="tpm" type="boolean" falsevalue="" truevalue="tpm" label="TPKM"/> | |
| 278 <param name="min_covered_fraction" type="integer" min="0" optional="true" | |
| 279 label="Min covered fraction" help="Genomes with less coverage than this reported as having zero coverage. Default: 10"/> | |
| 280 <param name="contig_end_exclusion" type="integer" min="0" optional="true" | |
| 281 label="Contig end exclusion" help="Exclude bases at the ends of reference sequences from calculation. Default: 75"/> | |
| 282 </section> | 313 </section> |
| 283 </xml> | 314 </xml> |
| 284 <xml name="out"> | 315 <xml name="cov_method_options"> |
| 285 <section name="out" title="Output options" expanded="false"> | 316 <option value="trimmed_mean">trimmed_mean: Average number of aligned reads overlapping each position after removing the most deeply and shallow-ly covered positions. </option> |
| 286 <param name="output_format" type="select" label="Shape of output" help="'Sparse' for long format, 'dense' for species-by-site. Default: dense]"> | 317 <option value="coverage_histogram">coverage_histogram: Histogram of coverage depths</option> |
| 287 <option value="dense" selected="true">Dense</option> | 318 <option value="covered_bases">covered_bases: Number of bases covered by 1 or more reads</option> |
| 288 <option value="sparse">Sparse</option> | 319 <option value="variance">variance: Variance of coverage depths</option> |
| 289 </param> | 320 <option value="length">length: Length of each contig in base pairs</option> |
| 290 <param name="no_zeros" type="boolean" truevalue="--no-zeros" falsevalue="" optional="true" label="Omit printing of genomes that have zero coverage" /> | 321 <option value="count">count: Number of reads aligned toq each contig. Note that a single read may be aligned to multiple contigs with supplementary alignments</option> |
| 291 <param argument="--dereplication-output-cluster-definition" type="boolean" truevalue="--dereplication-output-cluster-definition" falsevalue="" label="Output a file of representative TAB member lines." /> | 322 <option value="metabat">metabat: ("MetaBAT adjusted coverage") Coverage as defined in Kang et al 2015</option> |
| 292 <param argument="--dereplication-output-representative-fasta-directory-copy" type="boolean" truevalue="--dereplication-output-representative-fasta-directory-copy" falsevalue="" label="Output representative genomes" /> | 323 <option value="reads_per_base">reads_per_base: Number of reads aligned divided by the length of the contig</option> |
| 293 </section> | 324 <option value="rpkm">rpkm: Reads mapped per kilobase of contig, per million mapped reads</option> |
| 325 <option value="tpm">tpm: Transcripts Per Million as described in Li et al 2010</option> | |
| 326 </xml> | |
| 327 <xml name="coverage_params"> | |
| 328 <param argument="--trim-min" type="integer" min="0" value="5" label="Smallest fraction of positions to remove when calculating" help="Only used with trimmed_mean method"/> | |
| 329 <param argument="--trim-max" type="integer" min="0" value="95" label="Maximum fraction of positions to remove when calculating" help="Only used with trimmed_mean method"/> | |
| 330 <param argument="--min-covered-fraction" type="integer" min="0" value="10" label="Minimum covered fraction" help="Genomes with less coverage than this reported as having zero coverage"/> | |
| 331 <param argument="--contig-end-exclusion" type="integer" min="0" value="75" label="Base to exclude at contig ends" help="Bases at the ends of reference sequences will be excluded from calculation"/> | |
| 332 </xml> | |
| 333 <xml name="output_format"> | |
| 334 <param argument="--output-format" type="select" label="Shape of output"> | |
| 335 <option value="dense" selected="true">Dense for species-by-site</option> | |
| 336 <option value="sparse">Sparse for long format</option> | |
| 337 </param> | |
| 294 </xml> | 338 </xml> |
| 295 <xml name="citations"> | 339 <xml name="citations"> |
| 296 <citations> | 340 <citations> |
| 297 <yield /> | 341 <yield /> |
| 298 </citations> | 342 </citations> |