Mercurial > repos > nml > spades
diff spades.xml @ 14:74f20c988994 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
| author | iuc |
|---|---|
| date | Sun, 23 Jan 2022 21:31:26 +0000 |
| parents | b7829778729f |
| children | d2d1df21dfb9 |
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--- a/spades.xml Mon Sep 20 09:55:41 2021 +0000 +++ b/spades.xml Sun Jan 23 21:31:26 2022 +0000 @@ -1,359 +1,720 @@ -<tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy1"> - <description>genome assembler for regular and single-cell projects</description> - <xrefs> - <xref type="bio.tools">spades</xref> - </xrefs> +<tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>genome assembler for genomes of regular and single-cell projects</description> <macros> <import>macros.xml</import> </macros> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">spades</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - <regex match="Cannot allocate memory" - source="stdout" - level="fatal_oom" - description="Out of memory error occurred" /> - <regex match="The reads contain too many k-mers to fit into available memory" - source="stdout" - level="fatal_oom" - description="Out of memory error occurred" /> - </stdio> - <command> - <![CDATA[ - ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"><![CDATA[ + +#set $library = 1 - if [ -n "\$GALAXY_MEMORY_MB" ]; then - GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 )); - fi && +@PREPROCESS_INPUT_FILES_MAIN@ +#if $additional_reads.selector == 'true' + @PREPROCESS_INPUT_FILES_ADDITIONAL@ +#end if +@PREPROCESS_NANOPORE_PACBIO_FILES@ +@PREPROCESS_CONTIGS_FILES@ +@PREPROCESS_SANGER_FILES@ - spades.py -o . --tmp-dir "\${TMPDIR:-.}" --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250} - #if not $kmer_choice.auto_kmer_choice: - -k "$kmer_choice.kmers" - #end if - #if $cov.state == "auto": - --cov-cutoff 'auto' - #elif $cov.state == "value": - --cov-cutoff '$cov.cutoff' +## run +spades.py + $operation_mode + -o 'output' + @RESOURCES@ + @INPUT_READS_MAIN@ + #if $additional_reads.selector == 'true' + @INPUT_READS_ADDITIONAL@ #end if - $iontorrent - ## Sequence files, libraries - #for $i, $library in enumerate( $libraries, start=1 ) - #if str( $library.lib_type ) == "paired_end": - #set prefix = 'pe' - #elif str( $library.lib_type ) == "mate_paired": - #set prefix = 'mp' - #elif str( $library.lib_type ) == "nxmate_paired": - #set prefix = 'nxmate' - #else: - #set prefix = 'hqmp' - #end if - --$prefix$i-$library.orientation - #for $file in $library.files - #if $file.file_type.type == "separate" - --$prefix$i-1 $file.file_type.fwd_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.fwd_reads - --$prefix$i-2 $file.file_type.fwd_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.rev_reads - #elif $file.file_type.type == "interleaved" - --$prefix$i-12 $file.file_type.interleaved_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.interleaved_reads - #elif $file.file_type.type == "merged" - --$prefix$i-m $file.file_type.merged_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.merged_reads - #elif $file.file_type.type == "unpaired" - --$prefix$i-s $file.file_type.unpaired_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.unpaired_reads - #elif $file.file_type.type == "paired-collection" - --$prefix$i-1 $file.file_type.fastq_collection.forward.extension.replace('fastqsanger', 'fastq'):$file.file_type.fastq_collection.forward - --$prefix$i-2 $file.file_type.fastq_collection.reverse.extension.replace('fastqsanger', 'fastq'):$file.file_type.fastq_collection.reverse - #end if - #end for - #end for - #for $read in $pacbio_reads: - #if $read: - --pacbio fastq:$read - #end if - #end for - #for $read in $nanopore_reads: - #if $read: - --nanopore fastq:$read - #end if - #end for - #for $read in $sanger_reads: - #if $read: - --sanger $read.extension.replace('fastqsanger', 'fastq'):$read - #end if - #end for - #for $contig in $trusted_contigs: - #if $contig: - --trusted-contigs $contig.extension.replace('fastqsanger', 'fastq'):$contig - #end if - #end for - #for $contig in $untrusted_contigs: - #if $contig: - --untrusted-contigs $contig.extension.replace('fastqsanger', 'fastq'):$contig - #end if - #end for - && python '$write_tsv_script' < contigs.fasta > '$out_contig_stats' - && python '$write_tsv_script' < scaffolds.fasta > '$out_scaffold_stats' - ]]> - </command> + ## additional reads + @NANOPORE_PACBIO@ + @SANGER@ + @CONTIGS@ + ## parameter + --cov-cutoff $cov_cond.cov_cutoff + @KMER@ + @PIPELINE_OPTIONS@ + @PHREDOFFSET@ - <configfiles> - <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python -import sys,re -search_str = r'^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$' -replace_str = r'\1_\2\t\3\t\4' -cmd = re.compile(search_str) -sys.stdout.write('#name\tlength\tcoverage\n') -for i,line in enumerate(sys.stdin): - if cmd.match(line): - sys.stdout.write(cmd.sub(replace_str,line)) -]]> - </configfile> - </configfiles> - + ## postprocessing + @STATS@ + @CORRECTED@ + ]]></command> <inputs> - <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean"> - <option value="false">No</option> - <option value="true">Yes</option> - </param> - <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" /> - <param argument="--careful" checked="True" falsevalue="" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." label="Careful correction?" name="careful" truevalue="--careful" type="boolean" /> - <conditional name="kmer_choice"> - <param checked="False" falsevalue="false" help="k-mer choices can be chosen by SPAdes instead of being entered manually" label="Automatically choose k-mer values" name="auto_kmer_choice" truevalue="true" type="boolean" /> - <when value="false"> - <param help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." label="K-mers to use, separated by commas" name="kmers" type="text" value="21,33,55" /> - </when> - <when value="true" /> - </conditional> - <conditional name="cov"> - <param label="Coverage Cutoff" name="state" type="select"> - <option value="off">Off</option> - <option value="value">User Specific</option> - <option value="auto">Auto</option> - </param> - <when value="off" /> - <when value="value"> - <param help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" label="Coverage cutoff value" name="cutoff" type="float" value="" /> - </when> - <when value="auto" /> - </conditional> - <param checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" /> - <repeat help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided." min="1" max="9" name="libraries" title="Libraries"> - <param label="Library type" name="lib_type" type="select"> - <option value="paired_end">Paired-end / Single reads</option> - <option value="mate_paired">Mate pairs</option> - <option value="high_mate_paired">High Quality Mate pairs</option> - <option value="nxmate_paired">Lucigen NxMate pairs</option> - </param> - <param label="Orientation" name="orientation" type="select"> - <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option> - <option value="rf"><![CDATA[<- -> (rf)]]></option> - <option value="ff"><![CDATA[-> -> (ff)]]></option> - </param> - <repeat min="1" name="files" title="Files"> - <conditional name="file_type"> - <param label="Select file format" name="type" type="select"> - <option value="separate">Separate input files</option> - <option value="interleaved">Interleaved files</option> - <option value="merged">Merged files</option> - <option value="unpaired">Unpaired/Single reads</option> - <option value="paired-collection">Paired List Collection</option> - </param> - <when value="separate"> - <param format="@INTYPES@" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" /> - <param format="@INTYPES@" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" /> - </when> - <when value="interleaved"> - <param format="@INTYPES@" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" /> - </when> - <when value="merged"> - <param format="@INTYPES@" help="FASTQ format" label="Merged paired reads" name="merged_reads" type="data" /> - </when> - <when value="unpaired"> - <param format="@INTYPES@" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" /> - </when> - <when value="paired-collection"> - <param collection_type="paired" format="@INTYPES@" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" /> - </when> - </conditional> - </repeat> - </repeat> - <param optional="true" format="@INTYPES@" label="PacBio CLR reads" multiple="true" name="pacbio_reads" type="data" /> - <param optional="true" format="@INTYPES@" label="Nanopore reads" multiple="true" name="nanopore_reads" type="data" /> - <param optional="true" format="@INTYPES@" label="Sanger reads" multiple="true" name="sanger_reads" type="data" /> - <param optional="true" format="@INTYPES@" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" /> - <param optional="true" format="@INTYPES@" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" /> - <param name="contig_graph_out" type="boolean" checked="False" label="Output final assembly graph (contigs)?" help="Will output the final assembly graph (contigs) in fastg format for visualisation" /> - <param name="scaffold_graph_out" type="boolean" checked="False" label="Output final assembly graph with scaffolds?" help="Will output the final assembly graph with scaffold information in gfa format for visualisation" /> + <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/> + <expand macro="input_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)"/> + <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)"/> + <section name="arf" title="Additional read files"> + <expand macro="nanopore_pacbio"/> + <expand macro="sanger"/> + <expand macro="contigs"/> + </section> + <expand macro="pipeline_options"> + <option value="--sc">Single cell mode: required for MDA (single-cell) data (--sc)</option> + <option value="--isolate">Isolate: highly recommended for high-coverage isolate and multi-cell data (--isolate)</option> + <option value="--careful">Careful: ties to reduce the number of mismatches and short indels. Only recommended for small genomes (--careful)</option> + <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option> + </expand> + <expand macro="covcutoff"/> + <expand macro="kmer" help="If --sc is set the default values are 21,33,55. For multicell datasets K values are automatically selected using maximum read length."/> + <expand macro="phred"/> + <expand macro="optional_output"/> </inputs> - <outputs> - <data format="tabular" label="${tool.name} on ${on_string}: contig stats" name="out_contig_stats" > - <actions> - <action name="column_names" type="metadata" default="name,length,coverage"/> - </actions> - </data> - <data format="tabular" label="${tool.name} on ${on_string}: scaffold stats" name="out_scaffold_stats" > - <actions> - <action name="column_names" type="metadata" default="name,length,coverage"/> - </actions> - </data> - <data format="fasta" from_work_dir="contigs.fasta" label="${tool.name} on ${on_string}: contigs (fasta)" name="out_contigs" /> - <data format="fasta" from_work_dir="scaffolds.fasta" label="${tool.name} on ${on_string}: scaffolds (fasta)" name="out_scaffolds" /> - <data format="txt" from_work_dir="spades.log" label="${tool.name} on ${on_string}: log" name="out_log" /> - <data format="txt" from_work_dir="assembly_graph.fastg" label="${tool.name} on ${on_string}: assembly graph" name="contig_graph"> - <filter>contig_graph_out</filter> - </data> - <data format="txt" from_work_dir="assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: assembly graph with scaffolds" name="scaffold_graph"> - <filter>scaffold_graph_out</filter> - </data> + <expand macro="out_ag"/> + <expand macro="out_ags"/> + <expand macro="out_cn"/> + <expand macro="out_cp"/> + <expand macro="out_cr"/> + <expand macro="out_cs"/> + <expand macro="out_l"/> + <expand macro="out_sc"/> + <expand macro="out_sp"/> + <expand macro="out_ss"/> </outputs> <tests> - <test> <!-- Test 1 - basic test with k=33 --> - <param name="sc" value="false" /> - <param name="careful" value="false" /> - <param name="kmers" value="33" /> - <param name="lib_type" value="paired_end" /> - <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> - <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" /> - <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> - <output name="out_contig_stats"> + <!-- + used in a test: + single library: 12, 1, 2 + multiple libraries: s, pe#-12, pe#-1, pe#-2, pe#-<or> + k, phred-offset, disablerr, iontorrent, careful, isolate, only-assembler, only-error-correction, sc + + not used in a test: + multiple libraries: pe#-m, pe#-s, mp#-12, mp#-1, mp#-2, mp#-<or>, mp#-s, hqmp#-12, hqmp#-1, hqmp#-2, hqmp#-s, hqmp#-<or>, nxmate#-1, nxmate-#2 + --> + + <!-- #1 single, interlaced, fastq.gz, default parameters --> + <test expect_num_outputs="4"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired_interlaced"/> + <param name="input1" value="ecoli_1K.fastq.gz"/> + </conditional> + <output name="out_ag"> + <assert_contents> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE_.+"/> + </assert_contents> + </output> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="2"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000.+"/> + </assert_contents> + </output> + </test> + <!-- #2 single, separate, fastq, custom parameters --> + <test expect_num_outputs="9"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired"/> + <param name="input1" value="ecoli_1K_1.fastq.gz"/> + <param name="input2" value="ecoli_1K_2.fastq.gz"/> + </conditional> + <param name="mode_sel" value="--isolate,--disable-rr,--iontorrent"/> + <conditional name="cov_cond"> + <param name="cov_cutoff" value="auto"/> + </conditional> + <conditional name="kmer_cond"> + <param name="kmer_sel" value="manual"/> + <param name="manual" value="33"/> + </conditional> + <param name="phred_offset" value="33"/> + <param name="optional_output" value="ag,ags,cn,cp,cs,sc,sp,ss,l"/> + <output name="out_ag"> + <assert_contents> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE_.+"/> + </assert_contents> + </output> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="1"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_cp"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + <output name="out_cs"> + <assert_contents> + <has_n_lines n="1"/> + <has_text_matching expression="#name	length	coverage"/> + </assert_contents> + </output> + <output name="out_l"> + <assert_contents> + <has_text_matching expression="Thank you for using SPAdes!"/> + </assert_contents> + </output> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + <output name="out_sp"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + <output name="out_ss"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + </test> + <!-- #3 single, separate, fasta, default parameters --> + <test expect_num_outputs="4"> + <param name="operation_mode" value="--only-assembler"/> + <conditional name="singlePaired"> + <param name="sPaired" value="paired"/> + <param name="input1" value="ecoli_1K_1.fastq.gz"/> + <param name="input2" value="ecoli_1K_2.fastq.gz"/> + </conditional> + <output name="out_ag"> + <assert_contents> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE_.+"/> + </assert_contents> + </output> + <output name="out_ags"> <assert_contents> - <has_text_matching expression="NODE_1\t1000"/> + <has_n_lines n="2"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000.+"/> + </assert_contents> + </output> + </test> + <!-- #4 multiple, single & paired-end within same library: careful mode --> + <test expect_num_outputs="4"> + <conditional name="singlePaired"> + <param name="sPaired" value="single"/> + <param name="input1" value="ecoli_1K.fastq.gz"/> + </conditional> + <conditional name="additional_reads"> + <param name="selector" value="true"/> + <conditional name="singlePaired"> + <param name="sPaired" value="paired"/> + <param name="input1" value="ecoli_1K_1.fastq.gz"/> + <param name="input2" value="ecoli_1K_2.fastq.gz"/> + </conditional> + </conditional> + <param name="mode_sel" value="--careful"/> + <output name="out_ag"> + <assert_contents> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE_.+"/> + </assert_contents> + </output> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="2"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000.+"/> + </assert_contents> + </output> + </test> + <!-- #5 multiple, single & paired-end in different libraries --> + <test expect_num_outputs="4"> + <param name="operation_mode" value="--only-assembler"/> + <conditional name="singlePaired"> + <param name="sPaired" value="single"/> + <param name="input1" value="ecoli_1K.fastq.gz"/> + </conditional> + <conditional name="additional_reads"> + <param name="selector" value="true"/> + <conditional name="singlePaired"> + <param name="sPaired" value="paired"/> + <param name="input1" value="ecoli_1K_1.fastq.gz"/> + <param name="input2" value="ecoli_1K_2.fastq.gz"/> + </conditional> + </conditional> + <param name="mode_sel" value="--careful"/> + <output name="out_ag"> + <assert_contents> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE_.+"/> + </assert_contents> + </output> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="2"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000.+"/> + </assert_contents> + </output> + </test> + <!-- #6 only corrected reads are created as an output --> + <test expect_num_outputs="2"> + <param name="operation_mode" value="--only-error-correction"/> + <conditional name="singlePaired"> + <param name="sPaired" value="paired_interlaced"/> + <param name="input1" value="ecoli_1K.fastq.gz"/> + </conditional> + <param name="mode_sel" value="--careful"/> + <param name="optional_output" value="cr,l"/> + <output_collection name="out_cr" type="list" count="3"> + <element name="ecoli_1K.fastq.gz_1.00.0_0.cor"> + <assert_contents> + <has_size value="130317" delta="1000"/> + </assert_contents> + </element> + <element name="ecoli_1K.fastq.gz_2.00.0_0.cor"> + <assert_contents> + <has_size value="130317" delta="1000"/> + </assert_contents> + </element> + <element name="ecoli_1K.fastq.gz__unpaired.00.0_0.cor"> + <assert_contents> + <has_size value="20" delta="5"/> + </assert_contents> + </element> + </output_collection> + <output name="out_l"> + <assert_contents> + <has_text_matching expression="Thank you for using SPAdes!"/> </assert_contents> </output> </test> - <test> <!-- Test 2 - basic test with k=33 fasta input --> - <param name="sc" value="false" /> - <param name="onlyassembler" value="true"/> - <param name="careful" value="false" /> - <param name="kmers" value="33" /> - <param name="lib_type" value="paired_end" /> - <param ftype="fasta" name="fwd_reads" value="ecoli_1K_1.fasta" /> - <param ftype="fasta" name="rev_reads" value="ecoli_1K_2.fasta" /> - <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> - <output name="out_contig_stats"> + <!-- #7 only corrected reads are created as an output --> + <test expect_num_outputs="2"> + <param name="operation_mode" value="--only-error-correction"/> + <conditional name="singlePaired"> + <param name="sPaired" value="paired_interlaced"/> + <param name="input1" value="ecoli_1K.fastq.gz"/> + </conditional> + <param name="mode_sel" value="--careful,--sc"/> + <param name="optional_output" value="cr,l"/> + <output_collection name="out_cr" type="list" count="3"> + <element name="ecoli_1K.fastq.gz_1.00.0_0.cor"> + <assert_contents> + <has_size value="130317" delta="1000"/> + </assert_contents> + </element> + <element name="ecoli_1K.fastq.gz_2.00.0_0.cor"> + <assert_contents> + <has_size value="130317" delta="1000"/> + </assert_contents> + </element> + <element name="ecoli_1K.fastq.gz__unpaired.00.0_0.cor"> + <assert_contents> + <has_size value="20" delta="5"/> + </assert_contents> + </element> + </output_collection> + <output name="out_l"> <assert_contents> - <has_text_matching expression="NODE_1\t1000"/> + <has_text_matching expression="Thank you for using SPAdes!"/> + </assert_contents> + </output> + </test> + <!-- #8 --> + <test expect_num_outputs="4"> + <param name="operation_mode" value="--only-assembler"/> + <conditional name="singlePaired"> + <param name="sPaired" value="paired_interlaced"/> + <param name="input1" value="ecoli_1K.fastq.gz"/> + </conditional> + <param name="mode_sel" value="--sc"/> + <output name="out_ag"> + <assert_contents> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE_7_length_1000_cov_140.639153"/> + </assert_contents> + </output> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="2"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000.+"/> </assert_contents> </output> </test> - <test> <!-- Test 3 - basic test with k=33 and gzipped input --> - <param name="sc" value="false" /> - <param name="careful" value="false" /> - <param name="kmers" value="33" /> - <param name="lib_type" value="paired_end" /> - <param ftype="fastq.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" /> - <param ftype="fastq.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" /> - <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> - <output name="out_contig_stats"> + <!-- #9 only corrected reads are created as an output --> + <test expect_num_outputs="2"> + <param name="operation_mode" value="--only-error-correction"/> + <conditional name="singlePaired"> + <param name="sPaired" value="paired_interlaced"/> + <param name="input1" value="ecoli_1K.fastq.gz"/> + </conditional> + <param name="optional_output" value="cr,l"/> + <output_collection name="out_cr" type="list" count="3"> + <element name="ecoli_1K.fastq.gz_1.00.0_0.cor"> + <assert_contents> + <has_size value="130317" delta="1000"/> + </assert_contents> + </element> + <element name="ecoli_1K.fastq.gz_2.00.0_0.cor"> + <assert_contents> + <has_size value="130317" delta="1000"/> + </assert_contents> + </element> + <element name="ecoli_1K.fastq.gz__unpaired.00.0_0.cor"> + <assert_contents> + <has_size value="20" delta="5"/> + </assert_contents> + </element> + </output_collection> + <output name="out_l"> <assert_contents> - <has_text_matching expression="NODE_1\t1000"/> + <has_text_matching expression="Thank you for using SPAdes!"/> + </assert_contents> + </output> + </test> + <!-- #10 only corrected reads are created as an output --> + <test expect_num_outputs="2"> + <param name="operation_mode" value="--only-error-correction"/> + <conditional name="singlePaired"> + <param name="sPaired" value="paired_interlaced"/> + <param name="input1" value="ecoli_1K.fastq.gz"/> + </conditional> + <param name="mode_sel" value="--sc"/> + <param name="optional_output" value="cr,l"/> + <output_collection name="out_cr" type="list" count="3"> + <element name="ecoli_1K.fastq.gz_1.00.0_0.cor"> + <assert_contents> + <has_size value="130317" delta="1000"/> + </assert_contents> + </element> + <element name="ecoli_1K.fastq.gz_2.00.0_0.cor"> + <assert_contents> + <has_size value="130317" delta="1000"/> + </assert_contents> + </element> + <element name="ecoli_1K.fastq.gz__unpaired.00.0_0.cor"> + <assert_contents> + <has_size value="20" delta="5"/> + </assert_contents> + </element> + </output_collection> + <output name="out_l"> + <assert_contents> + <has_text_matching expression="Thank you for using SPAdes!"/> + </assert_contents> + </output> + </test> + <!-- #11 --> + <test expect_num_outputs="4"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired_interlaced"/> + <param name="input1" value="ecoli_1K.fastq.gz"/> + </conditional> + <param name="mode_sel" value="--sc"/> + <output name="out_ag"> + <assert_contents> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106"/> + </assert_contents> + </output> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="2"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000.+"/> </assert_contents> </output> </test> - <test> <!-- Test 4 - auto k --> - <param name="sc" value="false" /> - <param name="careful" value="false" /> - <param name="auto_kmer_choice" value="true" /> - <param name="lib_type" value="paired_end" /> - <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> - <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" /> - <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> - </test> - <test> <!-- Test 5 - k=77 --> - <param name="sc" value="false" /> - <param name="careful" value="false" /> - <param name="kmers" value="77" /> - <param name="lib_type" value="paired_end" /> - <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> - <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" /> - <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> - </test> - <test> <!-- Test 6 - test for extra graph outputs --> - <param name="sc" value="false" /> - <param name="careful" value="false" /> - <param name="kmers" value="33" /> - <param name="lib_type" value="paired_end" /> - <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> - <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" /> - <param name="contig_graph_out" value="true" /> - <param name="scaffold_graph_out" value="true" /> - <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> - <output name="out_contig_stats"> + <!-- #12 --> + <test expect_num_outputs="4"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired"/> + <param name="input1" value="ecoli_1K_1.fastq.gz"/> + <param name="input2" value="ecoli_1K_2.fastq.gz"/> + </conditional> + <param name="mode_sel" value="--sc,--careful"/> + <output name="out_ag"> <assert_contents> - <has_text_matching expression="NODE_1\t1000"/> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE_5_length_1000_cov_140.620106"/> + </assert_contents> + </output> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="2"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000.+"/> </assert_contents> </output> - <output name="contig_graph"> + </test> + <!-- #13 --> + <test expect_num_outputs="4"> + <param name="operation_mode" value="--only-assembler"/> + <conditional name="singlePaired"> + <param name="sPaired" value="paired"/> + <param name="input1" value="ecoli_1K_1.fastq.gz"/> + <param name="input2" value="ecoli_1K_2.fastq.gz"/> + </conditional> + <param name="mode_sel" value="--sc,--careful"/> + <output name="out_ag"> <assert_contents> - <has_text text=">EDGE_"/> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE\_.+"/> </assert_contents> </output> - <output name="scaffold_graph"> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="2"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> <assert_contents> - <has_text text="NODE_"/> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000.+"/> </assert_contents> </output> </test> - <test> <!-- Test 7 - basic test with k=33 and fastsanger input --> - <param name="sc" value="false" /> - <param name="careful" value="false" /> - <param name="kmers" value="33" /> - <param name="lib_type" value="paired_end" /> - <param ftype="fastqsanger" name="fwd_reads" value="ecoli_1K_1.fq" /> - <param ftype="fastqsanger" name="rev_reads" value="ecoli_1K_2.fq" /> - <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> - <output name="out_contig_stats"> + <!-- #14 interlaced, fastq.gz, hybrid assembly: nanopore, pacbio sanger and trustedcontigs --> + <test expect_num_outputs="4"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired_interlaced"/> + <param name="input1" value="ecoli_1K.fastq.gz"/> + </conditional> + <section name="arf"> + <param name="nanopore" value="ecoli_1K.fastq.gz"/> + <param name="pacbio" value="ecoli_1K.fastq.gz"/> + <param name="sanger" value="ecoli_1K.fastq.gz"/> + <param name="trusted_contigs" value="ecoli_1K.fasta.gz"/> + </section> + <assert_command> + <has_text text="--nanopore"/> + <has_text text="--pacbio"/> + <has_text text="--sanger"/> + <has_text text="--trusted-contigs"/> + </assert_command> + <output name="out_ag"> <assert_contents> - <has_text_matching expression="NODE_1\t1000"/> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE_.+"/> + </assert_contents> + </output> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="2"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000.+"/> </assert_contents> </output> </test> - <test> <!-- Test 8 - basic test with k=33 and fastsanger.gz input --> - <param name="sc" value="false" /> - <param name="careful" value="false" /> - <param name="kmers" value="33" /> - <param name="lib_type" value="paired_end" /> - <param ftype="fastqsanger.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" /> - <param ftype="fastqsanger.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" /> - <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> - <output name="out_contig_stats"> + <!-- #15 mate-pair reads orientation rf--> + <test expect_num_outputs="4"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired"/> + <param name="input1" value="ecoli_1K_1.fastq.gz"/> + <param name="input2" value="ecoli_1K_2.fastq.gz"/> + <param name="type_paired" value="hqmp"/> + <param name="orientation" value="rf"/> + </conditional> + <output name="out_ag"> + <assert_contents> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE_.+"/> + </assert_contents> + </output> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="1"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_sc"> <assert_contents> - <has_text_matching expression="NODE_1\t1000"/> + <has_n_lines n="0"/> + </assert_contents> + </output> + </test> + <!-- #16 high-quality mate-pair reads collection--> + <test expect_num_outputs="4"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired_collection"/> + <param name="input"> + <collection type="list:paired"> + <element name="ecoli.fastq"> + <collection type="paired"> + <element name="forward" value="ecoli_1K_1.fastq.gz" ftype="fastqsanger.gz"/> + <element name="reverse" value="ecoli_1K_2.fastq.gz" ftype="fastqsanger.gz"/> + </collection> + </element> + </collection> + </param> + <param name="type_paired" value="hqmp"/> + </conditional> + <output name="out_ag"> + <assert_contents> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE_.+"/> + </assert_contents> + </output> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="2"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="18"/> + <has_text_matching expression=">NODE\_1\_length\_1000.+"/> </assert_contents> </output> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ +.. class:: infomark + **What it does** -SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes. +@HELP_WID@ + +**Input** -This wrapper runs SPAdes, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. +@HELP_IN@ -**License** +**Output** -SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2. - -This wrapper is copyrighted by Philip Mabon and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. +@HELP_OUT_AG@ +@HELP_OUT_AGS@ +@HELP_OUT_C@ +@HELP_OUT_CP@ +@HELP_OUT_CR@ +@HELP_OUT_CS@ +@HELP_OUT_L@ +@HELP_OUT_S@ +@HELP_OUT_SP@ +@HELP_OUT_SS@ -This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. - -You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/. -** Acknowledgments ** +------------------- -Original wrapper developed by Lionel Guy. +.. class:: infomark -Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes. +**IonTorrent data** -Nicola Soranzo fixed various bugs. +@IONTORRENT@ + +------------------- -Simon Gladman added fastg optional outputs. -]]> - </help> - <citations> - <citation type="doi">10.1089/cmb.2012.0021</citation> - </citations> +.. class:: infomark + +**References** + +More information are available on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/spades>`_. + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1089/cmb.2012.0021</citation> + <citation type="doi">10.1007/978-3-642-37195-0_13</citation> + </expand> </tool>