Mercurial > repos > iuc > spades_metaviralspades
diff metaviralspades.xml @ 0:9346dcffaafc draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
| author | iuc |
|---|---|
| date | Sun, 23 Jan 2022 21:33:28 +0000 |
| parents | |
| children | 86f66ab58e14 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metaviralspades.xml Sun Jan 23 21:33:28 2022 +0000 @@ -0,0 +1,239 @@ +<tool id="spades_metaviralspades" name="metaviralSPAdes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>extract and assembly viral genomes from metagenomic 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 +spades.py --metaviral + -o 'output' + @RESOURCES@ + @INPUT_READS_MAIN@ + #if $additional_reads.selector == 'true' + @INPUT_READS_ADDITIONAL@ + #end if + ## reads + @NANOPORE_PACBIO@ + @SANGER@ + @CONTIGS@ + @ASSEMBLY_GRAPH@ + ## parameter + @KMER@ + @PHREDOFFSET@ + @PIPELINE_OPTIONS@ + ## postprocessing + @STATS@ + @CORRECTED@ + ]]></command> + <inputs> + <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"/> + <expand macro="sanger"/> + <expand macro="contigs"/> + <expand macro="assembly_graph"/> + </section> + <expand macro="kmer"/> + <expand macro="phred"/> + <expand macro="pipeline_options"> + <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> + <param name="optional_output" type="select" multiple="true" optional="false" label="Select optional output file(s)" help="Only shown in history if selected here and generated by the specific run."> + <option value="cn" selected="true">Contigs</option> + <option value="cs">Contigs stats</option> + <option value="cr">Corrected reads</option> + <option value="sc" selected="true">Scaffolds</option> + <option value="ss">Scaffolds stats</option> + <option value="l">Log</option> + </param> + </inputs> + <outputs> + <expand macro="out_cn"/> + <expand macro="out_cr"/> + <expand macro="out_cs"/> + <expand macro="out_l"/> + <expand macro="out_sc"/> + <expand macro="out_ss"/> + </outputs> + <tests> + <!-- + used in a test: + multiple libraries: s, pe#-12, pe#-1, pe#-2, pe#-<or> + k, phred-offset, disablerr, iontorrent, only-assembler, only-error-correction + --> + + <!-- #1 single, separate, fastq.gz, default parameters --> + <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> + <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, custom parameters --> + <test expect_num_outputs="6"> + <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="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="cn,cs,cr,sc,ss,l"/> + <output name="out_cn"> + <assert_contents> + <has_n_lines n="162"/> + <has_text_matching expression=">NODE\_1\_length\_9645\_cov\_.+"/> + </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="71752" delta="1000"/> + </assert_contents> + </element> + <element name="pl2.fq.gz.fastq.00.0_0.cor"> + <assert_contents> + <has_size value="71752" delta="1000"/> + </assert_contents> + </element> + <element name="pl_unpaired.00.0_0.cor"> + <assert_contents> + <has_size value="423" delta="100"/> + </assert_contents> + </element> + </output_collection> + <output name="out_sc"> + <assert_contents> + <has_n_lines n="162"/> + <has_text_matching expression=">NODE\_1\_length\_9645\_cov\_.+"/> + </assert_contents> + </output> + <output name="out_ss"> + <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> + </test> + <!-- #3 --> + <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="operation_mode" value="--only-assembler"/> + <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, only corrected reads are created as an output --> + <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> + <param name="operation_mode" value="--only-error-correction"/> + <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="71752" delta="1000"/> + </assert_contents> + </element> + <element name="pl2.fq.gz.fastq.00.0_0.cor"> + <assert_contents> + <has_size value="71752" delta="1000"/> + </assert_contents> + </element> + <element name="pl_unpaired.00.0_0.cor"> + <assert_contents> + <has_size value="423" 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@ + +metaplasmidSPAdes is a subtool for assembling plasmids from metagenomic data sets. + +**Input** + +@HELP_IN@ + +**Output** + +@HELP_OUT_C@ +@HELP_OUT_CS@ +@HELP_OUT_CR@ +@HELP_OUT_L@ +@HELP_OUT_S@ +@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/spades>`_. + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1101/gr.241299.118</citation> + </expand> +</tool>