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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit f53f7f297e551bf58e753752edd0dae5205bbc77
| author | iuc |
|---|---|
| date | Mon, 15 Apr 2024 19:38:22 +0000 |
| parents | a90db5dbaaf3 |
| children |
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<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> <xrefs> <xref type="bio.tools">spades</xref> </xrefs> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ #set $library = 1 @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@ @OMP_THREADS@ ## run spades.py $operation_mode -o 'output' @RESOURCES@ @INPUT_READS_MAIN@ #if $additional_reads.selector == 'true' @INPUT_READS_ADDITIONAL@ #end if ## additional reads @NANOPORE_PACBIO@ @SANGER@ @CONTIGS@ ## parameter #if $cov_cond.cov_cutoff == 'value': --cov-cutoff $cov_cond.manual #else: --cov-cutoff $cov_cond.cov_cutoff #end if @KMER@ @PIPELINE_OPTIONS@ @PHREDOFFSET@ ## postprocessing @STATS@ @CORRECTED@ ]]></command> <inputs> <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> <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> <!-- 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="2"/> <has_text_matching expression="#name	length	coverage"/> <has_text_matching expression="NODE_1	1000	225.723888"/> </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_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"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> <element name="ecoli_1K.fastq.gz_2.00.0_0"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> <element name="ecoli_1K.fastq.gz__unpaired.00.0_0"> <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> <!-- #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"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> <element name="ecoli_1K.fastq.gz_2.00.0_0"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> <element name="ecoli_1K.fastq.gz__unpaired.00.0_0"> <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> <!-- #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> <!-- #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"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> <element name="ecoli_1K.fastq.gz_2.00.0_0"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> <element name="ecoli_1K.fastq.gz__unpaired.00.0_0"> <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> <!-- #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"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> <element name="ecoli_1K.fastq.gz_2.00.0_0"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> <element name="ecoli_1K.fastq.gz__unpaired.00.0_0"> <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> <!-- #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_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> <!-- #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_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> <!-- #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_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> <!-- #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_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> <!-- #17 Fix stats script --> <test expect_num_outputs="1"> <conditional name="singlePaired"> <param name="sPaired" value="single"/> <param name="input1" value="ecoli_1K.fastq.gz"/> </conditional> <param name="optional_output" value="ss"/> <output name="out_ss"> <assert_contents> <has_n_lines n="2"/> <has_text text="NODE_1	1000	140.620106"/> <has_text_matching expression="#name	length	coverage"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** @HELP_WID@ **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@ ------------------- .. class:: infomark **IonTorrent data** @IONTORRENT@ ------------------- .. class:: infomark **References** More information are available on `github <https://github.com/ablab/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>