Mercurial > repos > iuc > spades_rnaviralspades
diff rnaviralspades.xml @ 0:5df83f4bad67 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
| author | iuc |
|---|---|
| date | Sun, 23 Jan 2022 21:31:52 +0000 |
| parents | |
| children | 249f6a28c751 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaviralspades.xml Sun Jan 23 21:31:52 2022 +0000 @@ -0,0 +1,359 @@ +<tool id="spades_rnaviralspades" name="rnaviralSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>de novo assembler for transcriptomes, metatranscriptomes and metaviromes</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_CONTIGS_FILES@ +@PREPROCESS_SANGER_FILES@ + +## run +spades.py --rnaviral + -o 'output' + @RESOURCES@ + @INPUT_READS_MAIN@ + #if $additional_reads.selector == 'true' + @INPUT_READS_ADDITIONAL@ + #end if + ## additional reads + @NANOPORE_PACBIO@ + @SANGER@ + @CONTIGS@ + ## parameter + @KMER@ + @PIPELINE_OPTIONS@ + @PHREDOFFSET@ + + ## postprocessing + @STATS@ + @CORRECTED@ + ]]></command> + <inputs> + <expand macro="input_files_all" format="fastq,fasta,fastq.gz,fastqsanger.gz,fasta.gz" label="FASTQ RNA-seq file(s)"/> + <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTQ RNA-seq file(s)"/> + <section name="arf" title="Additional read files"> + <expand macro="sanger"/> + <expand macro="nanopore_pacbio"/> + <expand macro="contigs"/> + </section> + <expand macro="pipeline_options"> + <option value="--iontorrent">Iontorrent: required when assembling IonTorrent data (--iontorrent)</option> + </expand> + <expand macro="kmer" help="By default rnaSPAdes uses 2 k-mer sizes, which are automatically detected using read length (approximately one third and half of the maximal read length). We recommend not to change this parameter because smaller k-mer sizes typically result in multiple chimeric (misassembled) transcripts."/> + <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: + 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, 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\_3\_length.+"/> + </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, all outputs --> + <test expect_num_outputs="10"> + <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 name="cov_cond"> + <param name="cov_cutoff" value="auto"/> + </conditional> + <param name="mode_sel" value="--disable-rr,--iontorrent"/> + <param name="phred_offset" value="33"/> + <param name="optional_output" value="ag,ags,cn,cp,cs,cr,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.+"/> + </assert_contents> + </output> + <output name="out_cp"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + <output_collection name="out_cr" type="list" count="2"> + <element name="ecoli_1K_1.fastq.gz.fastq0_0.cor"> + <assert_contents> + <has_size value="34468" delta="1000"/> + </assert_contents> + </element> + <element name="ecoli_1K_2.fastq.gz.fastq0_0.cor"> + <assert_contents> + <has_size value="34468" delta="1000"/> + </assert_contents> + </element> + </output_collection> + <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"> + <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_3_length_1000_cov_163.370137"/> + </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--> + <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> + <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> + <!-- #5 Multiple samples, different libraries: hybrid assembly: nanopore, pacbio --> + <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> + <param name="library_number" value="false"/> + </conditional> + + <output name="out_ag"> + <assert_contents> + <has_n_lines n="36"/> + <has_text_matching expression=">EDGE_3_length_1000_cov_326.740273"/> + </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[ +.. class:: infomark + +**What it does** + +@HELP_WID@ + +rnaviralSPAdes is a pipeline specially designed for de novo assembler tailored for RNA viral datasets (transcriptome, metatranscriptome and metavirome). + +**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>`_ and on the `project website <http://cab.spbu.ru/software/spades>`_. + ]]></help> + <expand macro="citations"/> +</tool>