| Previous changeset 2:f8cb3f0a19fa (2023-03-28) Next changeset 4:1dcea261abbe (2023-08-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2d02165f40a9f8206a69716b2302bc58f5364982 |
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modified:
coverm_contig.xml macros.xml |
| b |
| diff -r f8cb3f0a19fa -r c2a5823e4763 coverm_contig.xml --- a/coverm_contig.xml Tue Mar 28 08:36:07 2023 +0000 +++ b/coverm_contig.xml Wed Jul 26 07:35:24 2023 +0000 |
| [ |
| b'@@ -1,356 +1,450 @@\n <tool id="coverm_contig" name="CoverM contig" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n- <description>Calculate coverage of individual contigs</description>\n+ <description>Calculate read coverage per contig</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n+ <expand macro="bio_tools"/>\n <expand macro="requirements"/>\n <command><![CDATA[\n- #if $reads.read_type == "single" or $reads.read_type == "interleaved"\n- mkdir -p reads1 &&\n- #set file_paths1 = []\n- #for $input_file in $reads.single\n- \n- #set $fname = $input_file.element_identifier.replace(" ","_")\n- #set $file_path = \'reads1/\' + $fname\n- ln -s \'$input_file\' \'$file_path\' &&\n- $file_paths1.append($file_path)\n- #end for\n- #else if $reads.read_type == "bam"\n- mkdir -p bam &&\n- #set bam_files = []\n- #for $input_file in $reads.bam\n- \n- #set $fname = $input_file.element_identifier.replace(" ","_")\n- #set $file_path = \'bam/\' + $fname\n- ln -s \'$input_file\' \'$file_path\' &&\n- $bam_files.append($file_path)\n- #end for\n- #else if $reads.read_type == "paired"\n- mkdir -p paired_reads1 &&\n- #set fw_reads1 = []\n- #for $input_file in $reads.read1\n- \n- #set $fname = $input_file.element_identifier.replace(" ","_")\n- #set $file_path = \'paired_reads1/\' + str($fname)\n- ln -s \'$input_file\' \'$file_path\' &&\n- $fw_reads1.append($file_path)\n- #end for\n- #set rv_reads1 = []\n- #for $input_file in $reads.read2\n- \n- #set $fname = $input_file.element_identifier.replace(" ","_")\n- #set $file_path = \'paired_reads1/\' + str($fname)\n- ln -s \'$input_file\' \'$file_path\' &&\n- $rv_reads1.append($file_path)\n- #end for\n- #silent $fw_reads1.sort()\n- #silent $rv_reads1.sort()\n- #else\n- mkdir -p paired_reads &&\n- #set paired_reads1 = []\n- #for $i, $input_file in enumerate($reads.paired_reads)\n- #set $file_path = \'paired_reads/fw\' + str($i)\n- ln -s \'$input_file.forward\' \'$file_path\' &&\n- $paired_reads1.append($file_path)\n- #set $file_path = \'paired_reads/rv\' + str($i)\n- ln -s \'$input_file.reverse\' \'$file_path\' &&\n- $paired_reads1.append($file_path)\n- #end for\n- #end if \n- #if $add_reads.extra_read.read_type == "single" or $add_reads.extra_read.read_type == "interleaved"\n- mkdir -p add_reads1 &&\n- #set add_file_paths1 = []\n- #for $input_file in $add_reads.extra_read.single\n- #set $fname = $input_file.element_identifier.replace(" ","_")\n- #set $file_path = \'add_reads1/\' + $fname\n- ln -s \'$input_file\' \'$file_path\' &&\n- $add_file_paths1.append($file_path)\n- #end for\n- #else if $add_reads.extra_read.read_type == "bam"\n- mkdir -p add_bam &&\n- #set add_bam_files = []\n- #for $input_file in $reads.bam\n- #set $fname = $input_file.element_identifier.replace(" ","_")\n- #set $file_path = \'add_bam/\' + $fname\n- ln -s \'$input_file\' \'$file_path\' &&\n- $add_bam_files.append($file_path)\n- #end for\n- #else if $add_reads.extra_read.read_type == "paired"\n- mkdir -p add_paired_reads1 &&\n- #set add_fw_reads1 = []\n- #for $input_file in $add_reads.extra_read.read1\n- #set $fname = $input_file.element_identifier.replace(" ","_")'..b' <param name="bam_files" value="tpm_test.bam"/>\n+ <param name="sharded" value="" />\n+ </conditional>\n </conditional>\n+ <section name="alignment">\n+ <param name="min_read_aligned_length" value="0" />\n+ <param name="min_read_percent_identity" value="0.95" />\n+ <param name="min_read_aligned_percent" value="0" />\n+ <conditional name="proper_pairs_only">\n+ <param name="proper_pairs-only" value=""/>\n+ </conditional>\n+ <param name="exclude_supplementary" value=""/>\n+ </section>\n <section name="cov">\n- <param name="mean" value="true"/>\n- <param name="tpm" value="true"/>\n+ <param name="methods" value="mean,tpm"/>\n+ <param name="trim_min" value="5"/>\n+ <param name="trim_max" value="95"/>\n+ <param name="min_covered_fraction" value="10"/>\n+ <param name="contig_end_exclusion" value="75"/>\n </section>\n- <section name="out">\n- <param name="output_format" value="sparse"/>\n- </section> \n- <output name="output1" file="contig_test5.tsv" ftype="tsv" sort="true"/>\n- </test> \n- </tests>\n+ <param name="output_format" value="sparse"/>\n+ <output name="output" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="Contig"/>\n+ <has_text text="Mean"/>\n+ <has_text text="Sample"/>\n+ <has_text text="TPM"/>\n+ <has_text text="tpm_test"/>\n+ <has_text text="genome1~random_sequence_length_11000"/>\n+ <has_text text="genome2~seq1"/>\n+ <has_text text="genome3~random_sequence_length_11001"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <conditional name="mapped">\n+ <param name="mapped" value="mapped" />\n+ <conditional name="mode">\n+ <param name="mode" value="co"/>\n+ <param name="bam_files" value="tpm_test.bam"/>\n+ <param name="sharded" value="" />\n+ </conditional>\n+ </conditional>\n+ <section name="alignment">\n+ <param name="min_read_aligned_length" value="0" />\n+ <param name="min_read_percent_identity" value="0.95" />\n+ <param name="min_read_aligned_percent" value="0" />\n+ <conditional name="proper_pairs_only">\n+ <param name="proper_pairs-only" value=""/>\n+ </conditional>\n+ <param name="exclude_supplementary" value=""/>\n+ </section>\n+ <section name="cov">\n+ <param name="methods" value="mean,tpm"/>\n+ <param name="trim_min" value="5"/>\n+ <param name="trim_max" value="95"/>\n+ <param name="min_covered_fraction" value="10"/>\n+ <param name="contig_end_exclusion" value="75"/>\n+ </section>\n+ <param name="output_format" value="sparse"/>\n+ <output name="output" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="Contig"/>\n+ <has_text text="Mean"/>\n+ <has_text text="Sample"/>\n+ <has_text text="TPM"/>\n+ <has_text text="tpm_test"/>\n+ <has_text text="genome1~random_sequence_length_11000"/>\n+ <has_text text="genome2~seq1"/>\n+ <has_text text="genome3~random_sequence_length_11001"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n <help><![CDATA[\n .. class:: infomark\n \n' |
| b |
| diff -r f8cb3f0a19fa -r c2a5823e4763 macros.xml --- a/macros.xml Tue Mar 28 08:36:07 2023 +0000 +++ b/macros.xml Wed Jul 26 07:35:24 2023 +0000 |
| b |
| b'@@ -1,13 +1,17 @@\n <macros>\n+ <token name="@TOOL_VERSION@">0.6.1</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n+ <token name="@PROFILE@">22.01</token>\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">coverm</requirement>\n </requirements>\n </xml>\n- <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>\n- <token name="@TOOL_VERSION@">0.6.1</token>\n- <token name="@VERSION_SUFFIX@">0</token>\n- <token name="@PROFILE@">22.01</token>\n+ <xml name="bio_tools">\n+ <xrefs>\n+ <xref type="bio.tools">coverm</xref>\n+ </xrefs>\n+ </xml>\n <xml name="citation">\n <citations>\n <citation type="bibtex">\n@@ -22,275 +26,315 @@\n </citation>\n </citations>\n </xml>\n- <xml name="genome_opt">\n- <conditional name="genome">\n- <param name="ref_or_genome" type="select" label="Select if you want to specify additional genome files.">\n- <option value="genomic">yes</option>\n- <option value="none" selected="true">No (Only when BAM files are provided)</option>\n- </param>\n- <when value="none">\n- <param argument="--single-genome" type="boolean" truevalue="--single-genome" falsevalue="" checked="false" label="All contigs are from the same genome."/>\n- <param type="text" name="separator" optional="true" label="Character, that separates genome names from contig names in the reference file." >\n- <sanitizer>\n- <valid initial="string.punctuation">\n- </valid>\n- </sanitizer>\n- </param>\n+ <xml name="mapped">\n+ <param name="mapped" type="select" label="Have the reads already been mapped to contigs?">\n+ <option value="mapped">Yes (no read mapping algorithm will be undertaken)</option>\n+ <option value="not-mapped" selected="true">No</option>\n+ </param>\n+ </xml>\n+ <xml name="assembly_mode">\n+ <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)">\n+ <option value="individual">Individual assembly (1 contig file per sample)</option>\n+ <option value="co" selected="true">Co-assembly (1 contig file for several samples)</option>\n+ </param>\n+ </xml>\n+ <xml name="mapped_params">\n+ <conditional name="mode">\n+ <expand macro="assembly_mode"/>\n+ <when value="individual">\n+ <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)."/>\n+ </when>\n+ <when value="co">\n+ <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)."/>\n </when>\n- <when value="genomic">\n- <conditional name="genomic">\n- <param type="select" label="Reference genome source" name="source">\n- <option value="history" selected="true">History</option>\n- <option value="builtin">Built-in</option>\n- </param>\n- <when value="history">\n- <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" />\n- </when>\n- <when value="builtin">\n- <param type="select" name="fasta_builtin" multiple="true" lab'..b' label="Min covered fraction" help="Genomes with less coverage than this reported as having zero coverage. Default: 10"/>\n- <param name="contig_end_exclusion" type="integer" min="0" optional="true"\n- label="Contig end exclusion" help="Exclude bases at the ends of reference sequences from calculation. Default: 75"/>\n+ <param argument="--exclude-supplementary" type="boolean" truevalue="--exclude-supplementary" falsevalue="" checked="false"\n+ label="Exclude supplementary alignments"/>\n </section>\n </xml>\n- <xml name="out">\n- <section name="out" title="Output options" expanded="false">\n- <param name="output_format" type="select" label="Shape of output" help="\'Sparse\' for long format, \'dense\' for species-by-site. Default: dense]">\n- <option value="dense" selected="true">Dense</option>\n- <option value="sparse">Sparse</option>\n- </param>\n- <param name="no_zeros" type="boolean" truevalue="--no-zeros" falsevalue="" optional="true" label="Omit printing of genomes that have zero coverage" />\n- <param argument="--dereplication-output-cluster-definition" type="boolean" truevalue="--dereplication-output-cluster-definition" falsevalue="" label="Output a file of representative TAB member lines." />\n- <param argument="--dereplication-output-representative-fasta-directory-copy" type="boolean" truevalue="--dereplication-output-representative-fasta-directory-copy" falsevalue="" label="Output representative genomes" />\n- </section>\n+ <xml name="cov_method_options">\n+ <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>\n+ <option value="coverage_histogram">coverage_histogram: Histogram of coverage depths</option>\n+ <option value="covered_bases">covered_bases: Number of bases covered by 1 or more reads</option>\n+ <option value="variance">variance: Variance of coverage depths</option>\n+ <option value="length">length: Length of each contig in base pairs</option>\n+ <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>\n+ <option value="metabat">metabat: ("MetaBAT adjusted coverage") Coverage as defined in Kang et al 2015</option>\n+ <option value="reads_per_base">reads_per_base: Number of reads aligned divided by the length of the contig</option>\n+ <option value="rpkm">rpkm: Reads mapped per kilobase of contig, per million mapped reads</option>\n+ <option value="tpm">tpm: Transcripts Per Million as described in Li et al 2010</option>\n+ </xml>\n+ <xml name="coverage_params">\n+ <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"/>\n+ <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"/>\n+ <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"/>\n+ <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"/>\n+ </xml>\n+ <xml name="output_format">\n+ <param argument="--output-format" type="select" label="Shape of output">\n+ <option value="dense" selected="true">Dense for species-by-site</option>\n+ <option value="sparse">Sparse for long format</option>\n+ </param>\n </xml>\n <xml name="citations">\n <citations>\n' |