Mercurial > repos > nml > metaspades
diff metaspades.xml @ 6:a9b8c9e204ee draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
| author | iuc |
|---|---|
| date | Sun, 23 Jan 2022 21:33:56 +0000 |
| parents | 3ca2d2a9068c |
| children | f338e9942b27 |
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--- a/metaspades.xml Thu Sep 16 15:25:29 2021 +0000 +++ b/metaspades.xml Sun Jan 23 21:33:56 2022 +0000 @@ -1,116 +1,193 @@ -<tool id="metaspades" name="metaSPAdes" version="3.9.0.1"> - <description>assembler for metagenomics datasets</description> - <xrefs> - <xref type="bio.tools">metaspades</xref> - </xrefs> - <requirements> - <requirement type="package" version="3.9.0">spades</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command> - <![CDATA[ +<tool id="metaspades" name="metaSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>metagenome assembler</description> + <macros> + <import>macros.xml</import> + </macros> + <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@ - ## 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 - spades.py -o . --disable-gzip-output --meta $onlyassembler -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250} - #if not $kmer_choice.auto_kmer_choice: - -k "$kmer_choice.kmers" - #end if - ## Sequence files - #set num=1 - #if str( $lib_type ) == "paired_end": - #set prefix = 'pe' +## run +metaspades.py + -o 'output' + @RESOURCES@ + @INPUT_READS_MAIN@ + #if $additional_reads.selector == 'true' + @INPUT_READS_ADDITIONAL@ #end if - --$prefix$num-$orientation - #for $file in $files - #if $file.file_type.type == "separate" - --$prefix$num-1 fastq:$file.file_type.fwd_reads - --$prefix$num-2 fastq:$file.file_type.rev_reads - #elif $file.file_type.type == "interleaved" - --$prefix$num-12 fastq:$file.file_type.interleaved_reads - #elif $file.file_type.type == "paired-collection" - --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward - --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse - #end if - #end for - ]]> - </command> + ## reads + @NANOPORE_PACBIO@ + ## parameter + @KMER@ + @PHREDOFFSET@ + @PIPELINE_OPTIONS@ + ## postprocessing + @STATS@ + @CORRECTED@ + ]]></command> <inputs> - <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" /> - <conditional name="kmer_choice"> - <param name="auto_kmer_choice" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Automatically choose k-mer values" help="k-mer choices can be chosen by SPAdes instead of being entered manually" /> - <when value="false"> - <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" 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." /> - </when> - <when value="true" /> - </conditional> - <param name="lib_type" type="select" label="Library type"> - <option value="paired_end">Paired-end</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 name="files" title="Files" min="1"> - <conditional name="file_type"> - <param name="type" type="select" label="Select file format"> - <option value="separate">Separate input files</option> - <option value="interleaved">Interleaved files</option> - <option value="paired-collection">Paired List Collection</option> - </param> - <when value="separate"> - <param name="fwd_reads" type="data" format="fastq,fastq.gz" label="Forward reads" help="FASTQ format" /> - <param name="rev_reads" type="data" format="fastq,fastq.gz" label="Reverse reads" help="FASTQ format" /> - </when> - <when value="interleaved"> - <param name="interleaved_reads" type="data" format="fastq,fastq.gz" label="Interleaved paired reads" help="FASTQ format" /> - </when> - <when value="paired-collection"> - <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" format="fastq,fastq.gz" collection_type="paired" help="FASTQ format" /> - </when> - </conditional> - </repeat> + <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/> + <expand macro="input_additional_files_paired" format="fastq,fastq.gz,fastqsanger.gz" label="FASTQ file(s)"/> + <section name="arf" title="Additional read files"> + <expand macro="nanopore_pacbio"/> + </section> + <section name="arf" title="Additional read files"> + <expand macro="nanopore_pacbio"/> + </section> + <expand macro="kmer"/> + <expand macro="phred"/> + <expand macro="pipeline_options"> + <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option> + </expand> + <expand macro="optional_output"/> </inputs> <outputs> - <data name="out_contigs" format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" /> - <data name="out_scaffolds" format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" /> - <data name="out_fastg" format="txt" from_work_dir="assembly_graph.fastg" label="SPAdes assembly graph (fastg)" /> - <data name="out_log" format="txt" from_work_dir="spades.log" label="SPAdes log" /> + <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> - <param name="sc" value="false" /> - <param name="careful" value="false" /> - <param name="kmers" value="33,55" /> - <param name="lib_type" value="paired_end" /> - <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" /> - <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" /> - <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> + <!-- #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_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> - <param name="sc" value="false" /> - <param name="careful" value="false" /> - <param name="kmers" value="33,55" /> - <param name="lib_type" value="paired_end" /> - <param name="fwd_reads" value="ecoli_1K_1.fq.gz" ftype="fastq.gz" /> - <param name="rev_reads" value="ecoli_1K_2.fq.gz" ftype="fastq.gz" /> - <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> + <!-- #2 single, separate, fastq, default parameters --> + <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> + <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> + <!-- #3 only corrected reads are created as an output --> + <test expect_num_outputs="2"> + <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="Thank you for using SPAdes!"/> + </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> - <citations> - <citation type="doi">10.1089/cmb.2012.0021</citation> - </citations> +@HELP_WID@ + +metaSPAdes is a subtool for assembling metagenomic data sets. + +**Input** + +@HELP_IN@ + +**Output** + +@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@ + +**References** + +More information can be found on `github <https://github.com/ablab/spades>`_ and on the `project website <http://cab.spbu.ru/software/meta-spades>`_. + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1101/gr.213959.116</citation> + </expand> </tool>