Mercurial > repos > iuc > spades_plasmidspades
diff plasmidspades.xml @ 0:eabeb1a74dac draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
author | iuc |
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date | Sun, 23 Jan 2022 21:32:59 +0000 |
parents | |
children | 6aad515a5270 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plasmidspades.xml Sun Jan 23 21:32:59 2022 +0000 @@ -0,0 +1,382 @@ +<tool id="spades_plasmidspades" name="plasmidSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>extract and assembly plasmids from WGS data</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 + +@PREPROCESS_INPUT_FILES_MAIN@ +#if $additional_reads.selector == 'true' + @PREPROCESS_INPUT_FILES_ADDITIONAL@ +#end if +@PREPROCESS_NANOPORE_PACBIO_FILES@ +@PREPROCESS_SANGER_FILES@ +@PREPROCESS_CONTIGS_FILES@ +@PREPROCESS_ASSEMBLY_GRAPH_FILES@ + +## run +plasmidspades.py + $operation_mode + -o 'output' + @RESOURCES@ + @INPUT_READS_MAIN@ + #if $additional_reads.selector == 'true' + @INPUT_READS_ADDITIONAL@ + #end if + ## reads + @NANOPORE_PACBIO@ + @SANGER@ + @CONTIGS@ + @ASSEMBLY_GRAPH@ + ## parameter + --cov-cutoff $cov_cond.cov_cutoff + @KMER@ + @PIPELINE_OPTIONS@ + @PHREDOFFSET@ + ## postprocessing + @STATS@ + @CORRECTED@ + ]]></command> + <inputs> + <expand macro="operation_mode"/> + <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"/> + <expand macro="assembly_graph"/> + </section> + <expand macro="pipeline_options"> + <option value="--careful">Careful: tries 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"/> + <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, only-assembler, only-error-correction + + not used in a test: + single library: merged, s + 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 + pacbio, nanopore, sanger, trusted-contigs, untrusted-contigs, tslr + --> + + <!-- #1 single, separate, fastq.gz, default parameters --> + <test expect_num_outputs="4"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired"/> + <param name="input1" value="pl1.fq.gz"/> + <param name="input2" value="pl2.fq.gz"/> + </conditional> + <output name="out_ag"> + <assert_contents> + <has_n_lines n="326"/> + <has_text_matching expression=">EDGE_22_length_9689_cov_4.668331:EDGE_22_length_9689_cov_4.668331"/> + </assert_contents> + </output> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="3"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="163"/> + <has_text_matching expression=">NODE\_1\_length\_9689\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="163"/> + <has_text_matching expression=">NODE\_1\_length\_9689.+"/> + </assert_contents> + </output> + </test> + <!-- #2 single, separate, fastq, all outputs and custom parameters --> + <test expect_num_outputs="10"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired"/> + <param name="input1" value="pl1.fq.gz"/> + <param name="input2" value="pl2.fq.gz"/> + </conditional> + <conditional name="cov_cond"> + <param name="cov_sel" value="auto"/> + </conditional> + <param name="phred_offset" value="33"/> + <param name="optional_output" value="ag,ags,cn,cp,cr,cs,l,sc,sp,ss"/> + <output name="out_ag"> + <assert_contents> + <has_n_lines n="326"/> + <has_text_matching expression=">EDGE_.+"/> + </assert_contents> + </output> + <output name="out_ags"> + <assert_contents> + <has_n_lines n="3"/> + <has_text_matching expression="S.+"/> + </assert_contents> + </output> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="163"/> + <has_text_matching expression=">NODE.+"/> + </assert_contents> + </output> + <output name="out_cp"> + <assert_contents> + <has_n_lines n="4"/> + </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_collection name="out_cr" type="list" count="3"> + <element name="pl1.fq.gz.fastq.00.0_0.cor"> + <assert_contents> + <has_size value="72173" delta="1000"/> + </assert_contents> + </element> + <element name="pl2.fq.gz.fastq.00.0_0.cor"> + <assert_contents> + <has_size value="72173" delta="1000"/> + </assert_contents> + </element> + <element name="pl_unpaired.00.0_0.cor"> + <assert_contents> + <has_size value="392" delta="100"/> + </assert_contents> + </element> + </output_collection> + <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="163"/> + </assert_contents> + </output> + <output name="out_sp"> + <assert_contents> + <has_n_lines n="4"/> + </assert_contents> + </output> + <output name="out_ss"> + <assert_contents> + <has_n_lines n="1"/> + </assert_contents> + </output> + </test> + <!-- #3 multiple, single & paired-end, test dataset not valid --> + <test expect_num_outputs="1"> + <param name="operation_mode" value="--only-assembler"/> + <conditional name="singlePaired"> + <param name="sPaired" value="interlaced"/> + <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="pl1.fq.gz"/> + <param name="input2" value="pl2.fq.gz"/> + </conditional> + <param name="type_paired" value="mp"/> + <param name="orientation" value="rf"/> + </conditional> + <param name="mode_sel" value="--careful"/> + <param name="optional_output" value="l"/> + <output name="out_l"> + <assert_contents> + <has_text_matching expression="Thank you for using SPAdes!"/> + </assert_contents> + </output> + </test> + <!-- #4 test dataset not valid--> + <test expect_num_outputs="1"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired"/> + <param name="input1" value="pl1.fq.gz"/> + <param name="input2" value="pl2.fq.gz"/> + </conditional> + <param name="mode_sel" value="--careful"/> + <param name="optional_output" value="l"/> + <output name="out_l"> + <assert_contents> + <has_text_matching expression="Thank you for using SPAdes!"/> + </assert_contents> + </output> + </test> + <!-- #5 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"/> + <param name="input1" value="pl1.fq.gz"/> + <param name="input2" value="pl2.fq.gz"/> + </conditional> + <param name="optional_output" value="cr,l"/> + <output_collection name="out_cr" type="list" count="3"> + <element name="pl1.fq.gz.fastq.00.0_0.cor"> + <assert_contents> + <has_size value="72173" delta="1000"/> + </assert_contents> + </element> + <element name="pl2.fq.gz.fastq.00.0_0.cor"> + <assert_contents> + <has_size value="72173" delta="1000"/> + </assert_contents> + </element> + <element name="pl_unpaired.00.0_0.cor"> + <assert_contents> + <has_size value="392" delta="100"/> + </assert_contents> + </element> + </output_collection> + <output name="out_l"> + <assert_contents> + <has_text_matching expression="Thank you for using SPAdes!"/> + </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"/> + <param name="input1" value="pl1.fq.gz"/> + <param name="input2" value="pl2.fq.gz"/> + </conditional> + <param name="optional_output" value="cr,l"/> + <output_collection name="out_cr" type="list" count="3"> + <element name="pl1.fq.gz.fastq.00.0_0.cor"> + <assert_contents> + <has_size value="72173" delta="1000"/> + </assert_contents> + </element> + <element name="pl2.fq.gz.fastq.00.0_0.cor"> + <assert_contents> + <has_size value="72173" delta="1000"/> + </assert_contents> + </element> + <element name="pl_unpaired.00.0_0.cor"> + <assert_contents> + <has_size value="392" delta="100"/> + </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 hybrid assembly: nanpopore, pacbio, sanger, untrustedcontigs --> + <test expect_num_outputs="2"> + <conditional name="singlePaired"> + <param name="sPaired" value="paired"/> + <param name="input1" value="pl1.fq.gz"/> + <param name="input2" value="pl2.fq.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="untrusted_contigs" value="ecoli_1K.fasta.gz"/> + </section> + <assert_command> + <has_text text="--nanopore"/> + <has_text text="--pacbio"/> + <has_text text="--sanger"/> + <has_text text="--untrusted-contigs"/> + </assert_command> + <param name="mode_sel" value="--careful"/> + <param name="optional_output" value="cr,l"/> + <output_collection name="out_cr" type="list" count="3"> + <element name="pl1.fq.gz.fastq.00.0_0.cor"> + <assert_contents> + <has_size value="72173" delta="1000"/> + </assert_contents> + </element> + <element name="pl2.fq.gz.fastq.00.0_0.cor"> + <assert_contents> + <has_size value="72173" delta="1000"/> + </assert_contents> + </element> + <element name="pl_unpaired.00.0_0.cor"> + <assert_contents> + <has_size value="392" delta="100"/> + </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[ +.. class:: infomark + +**What it does** + +@HELP_WID@ + +plasmidSPAdes is a subtool for assembling plasmid 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/plasmid-spades>`_. + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1093/bioinformatics/btw493</citation> + </expand> +</tool>