| Previous changeset 0:0e2450894b69 (2018-12-07) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/savage commit b'6e7f074d80e0f35516e223b76e73f019ad45dd74\n'-dirty |
|
modified:
savage.xml |
| b |
| diff -r 0e2450894b69 -r 0793badf352c savage.xml --- a/savage.xml Fri Dec 07 14:30:00 2018 -0500 +++ b/savage.xml Wed Mar 20 11:05:31 2019 -0400 |
| [ |
| b'@@ -1,25 +1,26 @@\n <?xml version="1.0"?>\n <tool id="savage" version="@VERSION@+galaxy0" name="Assemble">\n- <description>viral haplotypes with SAVAGE</description>\n- <macros>\n- <token name="@SINGLE@">-s \'$input_type.input\'</token>\n- <token name="@PAIRED@">-p1 \'$input_type.forward\' -p2 \'$input_type.reverse\'</token>\n- <token name="@BOTH@">@SINGLE@ @PAIRED@</token>\n- <token name="@VERSION@">0.4.0</token>\n- <xml name="single_input">\n- <param name="input" argument="-s" type="data" format="fastq" label="Single-end reads" />\n- </xml>\n- <xml name="paired_input">\n- <param name="forward" argument="-p1" type="data" format="fastq" label="Forward reads" />\n- <param name="reverse" argument="-p2" type="data" format="fastq" label="Reverse reads" />\n- </xml>\n- </macros>\n- <requirements>\n- <requirement type="package" version="@VERSION@">savage</requirement>\n- </requirements>\n- <version_command><![CDATA[savage --help | grep \'^Version: \' | awk \'{print $2}\']]></version_command>\n- <command detect_errors="exit_code">\n- <![CDATA[\n+ <description>viral haplotypes with SAVAGE</description>\n+ <macros>\n+ <token name="@SINGLE@">-s \'$input_type.input\'</token>\n+ <token name="@PAIRED@">-p1 \'$input_type.forward\' -p2\n+ \'$input_type.reverse\'</token>\n+ <token name="@BOTH@">@SINGLE@ @PAIRED@</token>\n+ <token name="@VERSION@">0.4.0</token>\n+ <xml name="single_input">\n+ <param name="input" argument="-s" type="data" format="fastq" label="Single-end reads"/>\n+ </xml>\n+ <xml name="paired_input">\n+ <param name="forward" argument="-p1" type="data" format="fastq" label="Forward reads"/>\n+ <param name="reverse" argument="-p2" type="data" format="fastq" label="Reverse reads"/>\n+ </xml>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">\n+ savage</requirement>\n+ </requirements>\n+ <version_command><![CDATA[savage --help | grep \'^Version: \' | awk \'{print $2}\']]></version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n savage\n -t \\${GALAXY_SLOTS:-1} $revcomp\n #if $input_type.singles == \'single\':\n@@ -68,77 +69,75 @@\n $advanced.no_stage_a $advanced.no_stage_b $advanced.no_stage_c $advanced.no_overlaps $advanced.no_preprocessing\n $advanced.no_assembly $advanced.count_strains $advanced.ignore_subreads $advanced.keep_branches $advanced.diploid\n $advanced.no_filtering\n- ]]>\n- </command>\n- <inputs>\n- <conditional name="input_type" label="Input data formats">\n- <param name="singles" type="select" label="Type of reads">\n- <option value="paired">Paired reads</option>\n- <option value="single">Single-end reads</option>\n- <option value="both">Both single-end and paired</option>\n- </param>\n- <when value="single">\n- <expand macro="single_input" />\n- </when>\n- <when value="paired">\n- <expand macro="paired_input" />\n- </when>\n- <when value="both">\n- <expand macro="single_input" />\n- <expand macro="paired_input" />\n- </when>\n- </conditional>\n- <param argument="--ref" type="data" format="fasta" optional="true" label="Optional reference genome in fasta format" />\n- <param name="min_overlap_len" argument="-m" type="integer" value="" optional="true" label="Minimum overlap length between reads" help="By default this parameter is set to 60% of the average length of the sequencing reads used as input for SAVAGE. You can manually change this threshold using the this parameter. Increasing the minimal overlap length speeds up the algorithm and leads to a lower mismatch rate in the final contigs. It is recommended to set the minimal overlap length to be larger than the (expected) largest repetitive element in the target genomes. '..b'only relevant when running SAVAGE in de novo mode, i.e. without a reference FASTA. It specifies the error rate allowed when computing approximate suffix-prefix overlaps. By default it is equal to 50, meaning that up to 2% mismatches is allowed in the overlaps. This accounts for 1% sequencing errors. Increasing this parameter will slow down the algorithm, while decreasing will lead to a possibly incomplete overlap graph."/>\n+ <param argument="--diploid" type="boolean" truevalue="--diploid" falsevalue="" label="Diploid genome assembly"/>\n+ <param argument="--diploid_contig_len" type="integer" value="" optional="true" label="Minimum contig length required for diploid step contigs"/>\n+ <param argument="--diploid_overlap_len" type="integer" value="" optional="true" label="Minimum overlap length used in diploid assembly step"/>\n+ <param argument="--average_read_len" type="integer" value="" optional="true" label="Average length of the input reads" help="Will be computed from the input if not specified"/>\n+ <param argument="--no_filtering" type="boolean" truevalue="--no_filtering" falsevalue="" label="Disable kallisto-based filtering of contigs" help="By default, SAVAGE contigs are filtered after stages b and c based on Kallisto frequency estimates: all zero-abundance contigs are removed from the assembly. To disable this filtering procedure, enable this flag."/>\n+ <param argument="--max_tip_len" type="integer" value="100" optional="true" label="Maximum extension length for a sequence to be called a tip" help="Maximum extension length for a sequence to be called a tip in the overlap graph. By default this parameter is set to the average length of the input sequences. If you want to disable tip removal, set this parameter to 0. In general this will lead to a more fragmented assembly and is therefore not recommended."/>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="contigs" format="fasta" from_work_dir="contigs_stage_a.fasta" label="${tool.name} on ${on_string}: Contigs"/>\n+ <data name="haplotypes" format="fasta" from_work_dir="contigs_stage_c.fasta" label="${tool.name} on ${on_string}: Haplotyes"/>\n+ <data name="log" format="txt" from_work_dir="stage_c/pipeline.log" label="${tool.name} on ${on_string}: Log"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="singles" value="both"/>\n+ <param name="input" ftype="fastq" value="savage-in1.fq"/>\n+ <param name="forward" ftype="fastq" value="savage-in1-forward.fq"/>\n+ <param name="reverse" ftype="fastq" value="savage-in1-reverse.fq"/>\n+ <param name="split" value="1"/>\n+ <param name="merge_contigs" value="0"/>\n+ <param name="contig_len_stage_c" value="100"/>\n+ <param name="overlap_len_stage_c" value="100"/>\n+ <output name="contigs" ftype="fasta" file="savage-out1.fa"/>\n+ <output name="log" ftype="txt" file="savage-out1.txt" lines_diff="4"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n SAVAGE is a computational tool for reconstructing individual haplotypes of intra-host virus strains (a viral quasispecies) without the need for a high quality reference genome. SAVAGE makes use of either FM-index based data structures or ad-hoc consensus reference sequence for constructing overlap graphs from patient sample data. In this overlap graph, nodes represent reads and/or contigs, while edges reflect that two reads/contigs, based on sound statistical considerations, represent identical haplotypic sequence. Following an iterative scheme, a new overlap assembly algorithm that is based on the enumeration of statistically well-calibrated groups of reads/contigs then efficiently reconstructs the individual haplotypes from this overlap graph.\n-]]>\n- </help>\n- <citations>\n- <citation type="doi">doi:10.1101/gr.215038.116</citation>\n- </citations>\n-</tool>\n\\ No newline at end of file\n+]]></help>\n+ <citations>\n+ <citation type="doi">doi:10.1101/gr.215038.116</citation>\n+ </citations>\n+</tool>\n' |