srst2: srst2.xml comparison

comparison srst2.xml @ 0:36f105850c0d draft

planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27

author	iuc
date	Mon, 22 Aug 2022 19:12:11 +0000
parents
children	4e0b819bf73e

comparison

equal deleted inserted replaced

--1:000000000000
+:36f105850c0d
+<tool id="srst2" name="SRST2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<description>Short Read Sequence Typing for Bacterial Pathogens</description>
+<macros>
+<import>macros.xml</import>
+<token name="@FAST_A_Q_FORMATS@">fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
+</macros>
+<expand macro="requirements"/>
+<version_command>srst2 --version</version_command>
+<command detect_errors="exit_code"><![CDATA[
+#if $input.selector == "single"
+#set ext=$input.single_input.datatype.file_ext
+ln -s $input.single_input './input_read1.$ext' &&
+#else if $input.selector == "paired"
+#set ext_1=$input.paired_input1.datatype.file_ext
+#set ext_2=$input.paired_input2.datatype.file_ext
+ln -s $input.paired_input1 './input_read1.$ext_1' &&
+ln -s $input.paired_input2 './input_read2.$ext_2' &&
+#end if
+#for $i, $s in enumerate($prev_output)
+#if $s
+ln -s $s './$i-prev_output.txt' &&
+#end if
+#end for
+#for $i, $s in enumerate($use_gene_db.gene_db)
+#if $s
+ln -s $s './$i-gene_db.fasta' &&
+#end if
+#end for
+#if $use_mlst_db.selector == "yes"
+#set ext_3=$use_mlst_db.mlst_definitions.datatype.file_ext
+ln -s $use_mlst_db.mlst_db './mlst_db.fasta' &&
+ln -s $use_mlst_db.mlst_definitions './mlst_definitions.$ext_3' &&
+#end if
+srst2
+#if $input.selector == "single"
+--input_se './input_read1.$ext'
+--read_type ${input.read_type}
+#else if $input.selector == "paired"
+--input_pe './input_read1.$ext_1' './input_read2.$ext_2'
+$input.merge_paired
+--forward _read1
+--reverse _read2
+--read_type ${input.read_type}
+#end if
+#if $use_mlst_db.selector == "yes"
+--mlst_db './mlst_db.fasta'
+--mlst_definitions './mlst_definitions.$ext_3'
+--mlst_delimiter '$use_mlst_db.mlst_delimiter'
+--mlst_max_mismatch $use_mlst_db.mlst_max_mismatch
+--min_depth $use_mlst_db.min_depth
+--min_edge_depth $use_mlst_db.min_edge_depth
+#end if
+#if $use_gene_db.selector == "yes"
+--gene_db
+#for $i, $s in enumerate($use_gene_db.gene_db)
+#if $s
+'$i-gene_db.fasta'
+#end if
+#end for
+$use_gene_db.no_gene_details
+--gene_max_mismatch $use_gene_db.gene_max_mismatch
+--min_coverage $use_gene_db.min_coverage
+--max_divergence $use_gene_db.max_divergence
+#end if
+--prob_err $prob_err
+#if $truncation_score_tolerance
+--truncation_score_tolerance $truncation_score_tolerance
+#end if
+#if $stop_after
+--stop_after $stop_after
+#end if
+--max_unaligned_overlap $max_unaligned_overlap
+--mapq $mapq
+--baseq $baseq
+--output 'output'
+#if $prev_output
+--prev_output
+#for $i, $s in enumerate($prev_output)
+#if $s
+'$i-prev_output.txt'
+#end if
+#end for
+#end if
+#if 'log' in str($output_files_selector)
+--log
+#end if
+#if 'save_scores' in str($output_files_selector)
+--save_scores
+#end if
+#if 'report_new_consensus' in str($output_files_selector)
+--report_new_consensus
+#end if
+#if 'report_all_consensus' in str($output_files_selector)
+--report_all_consensus
+#end if
+#if 'keep_interim_alignment' in str($output_files_selector)
+--keep_interim_alignment
+#end if
+#if 'report_new_consensus' in str($output_files_selector) and $use_gene_db.selector == "yes" and $use_mlst_db.selector == "yes"
+&& mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput
+#end if
+#if $use_gene_db.selector == "yes" and  $use_gene_db.no_gene_details
+&& mkdir -p geneTypingOutput/ && cp output__genes__*__results.txt geneTypingOutput && cp output__fullgenes__*__results.txt geneTypingOutput
+#end if
+#if 'save_scores' in str($output_files_selector)
+&& mkdir -p scoresOutput/ && cp *.scores scoresOutput
+#end if
+#if $input.selector == "single" or $input.selector == "paired"
+&& mkdir -p bowtie2Alignments/ && cp *.sorted.bam bowtie2Alignments
+&& mkdir -p samtoolsPileup/ && cp output__input.*.pileup samtoolsPileup
+#end if
+]]></command>
+<inputs>
+<conditional name="input">
+<param name="selector" type="select" label="Reads files type for anaylsis">
+<option value="single">Single-end</option>
+<option value="paired">Paired-end</option>
+<option value="only_compiling_previous_results">Only Compiling Previous SRST2 Results</option>
+</param>
+<when value="single">
+<param name="single_input" type="data" format="@FAST_A_Q_FORMATS@" label="Single end read file(s) for analysing (may be gzipped)"/>
+<expand macro="read_type_options" />
+</when>
+<when value="paired">
+<param name="paired_input1" type="data" format="@FAST_A_Q_FORMATS@" label="Paired end read files for analysing (may be gzipped)"/>
+<param name="paired_input2" type="data" format="@FAST_A_Q_FORMATS@" label="Paired end read files for analysing (may be gzipped)"/>
+<param argument="--merge_paired" type="boolean" truevalue="--merge_paired" falsevalue="" checked="false" label="Do you want to merge the data to get a single result" help="Important only if all the input read sets belong to a single sample"/>
+<expand macro="read_type_options" />
+</when>
+<when value="only_compiling_previous_results">
+</when>
+</conditional>
+<conditional name="use_mlst_db">
+<param name="selector" type="select" label="Do you want to provide an MLST database of all allele sequences for the MLST scheme?">
+<option value="yes">Yes</option>
+<option value="no">No</option>
+</param>
+<when value="yes">
+<param argument="--mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/>
+<param argument="--mlst_definitions" type="data" format="tabular" label="ST definitions for MLST scheme" help="This is the file that tells you the ST number that is assigned to known combinations of alleles. Column 1 is the ST, and subsequent columns are the loci that make up the scheme."/>
+<param argument="--mlst_delimiter" type="text" value="-" label="Character(s) separating gene name from allele number in MLST database" help="E.g.'-', as in arcc-1">
+<sanitizer invalid_char="">
+<valid initial="string.letters,string.digits">
+<add value="\" />
+<add value="-" />
+<add value="/" />
+<add value="+" />
+<add value="=" />
+<add value=" " />
+<add value="_" />
+</valid>
+</sanitizer>
+<validator type="regex">[A-Za-z0-9 =-_/+]+</validator>
+</param>
+<param argument="--mlst_max_mismatch" type="integer" value="10" label="Maximum number of mismatches per read for MLST allele calling"/>
+<param argument="--min_depth" type="integer" value="5" label="Minimum mean depth to flag as dubious allele call"/>
+<param argument="--min_edge_depth" type="integer" value="2" label="Minimum edge depth to flag as dubious allele call"/>
+</when>
+<when value="no">
+</when>
+</conditional>
+<conditional name="use_gene_db">
+<param name="selector" type="select" label="Do you want to use a Gene database(s)?">
+<option value="yes">Yes</option>
+<option value="no">No</option>
+</param>
+<when value="yes">
+<param argument="--gene_db" type="data" optional="true" multiple="true" format="fasta" label="Gene database(s)" help="Fasta file/s for gene databases"/>
+<param argument="--no_gene_details" type="boolean" truevalue="" falsevalue="--no_gene_details" checked="false" label="Do you want reporting of gene typing?"/>
+<param argument="--gene_max_mismatch" type="integer" value="10" label="Maximum number of mismatches per read for gene detection and allele calling"/>
+<param argument="--min_coverage" type="integer" value="90" label="Minimum %coverage cutoff for gene reporting"/>
+<param argument="--max_divergence" type="integer" value="10" label="Maximum %divergence cutoff for gene reporting"/>
+</when>
+<when value="no">
+</when>
+</conditional>
+<param name="output_files_selector" type="select" label="Select all outputs you need" multiple="true">
+<option value="log">Save the log</option>
+<option value="save_scores">Report scores</option>
+<option value="report_new_consensus">Report the consensus allele if a matching alleles is not found</option>
+<option value="report_all_consensus">Report the consensus allele for the most likely allele</option>
+<option value="keep_interim_alignment">Keep interim files (sam and unsorted bam)</option>
+</param>
+<param argument="--prob_err" type="float" min="0" max="1" value="0.01" label="Probability of sequencing error"/>
+<param argument="--truncation_score_tolerance" optional="true" type="float" label="% increase in score allowed to choose non-truncated allele"/>
+<param argument="--stop_after" type="integer" optional="true" label="Stop mapping after this number of reads have been mapped" help="Leave empty to map all"/>
+<param argument="--max_unaligned_overlap" type="integer" value="10" label="Read discarded from alignment" help="if either of its ends has unaligned overlap with the reference that is longer than this value"/>
+<param argument="--mapq" type="integer" value="1" label="Samtools -q parameter (Minimum mapping quality)"/>
+<param argument="--baseq" type="integer" value="20" label="Samtools -Q parameter (Minimum base quality)"/>
+<param argument="--prev_output" type="data" format="tabular" multiple="true" optional="true" label="SRST2 results files to compile" help="Any new results from this run will also be incorporated"/>
+</inputs>
+<outputs>
+<data name="mlst_results" format="tabular" from_work_dir="output__mlst__mlst_db__results.txt" label="${tool.name} on ${on_string}: MLST Results">
+<filter>use_mlst_db['selector'] == "yes"</filter>
+</data>
+<collection name="gene_typing" type="list" label="${tool.name} on ${on_string}: Gene typing results files" >
+<discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutput" format="txt,tabular"/>
+<filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter>
+</collection>
+<data name="Compiled_gene_and_mlst_output" format="tabular" from_work_dir="output__compiledResults.txt" label="${tool.name} on ${on_string}: Compiled MLST and Gene databases Results">
+</data>
+<data name="all_consensus" format="fasta" from_work_dir="output.all_consensus_alleles.fasta" label="${tool.name} on ${on_string}: All consensus Results">
+<filter>"report_all_consensus" in output_files_selector</filter>
+</data>
+<collection name="new_consensus" type="list" label="${tool.name} on ${on_string}: New consensus Results" >
+<discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="allelesOutput" format="pileup"/>
+<filter>"report_new_consensus" in output_files_selector</filter>
+</collection>
+<collection name="scores_ofEachAllele" type="list" label="${tool.name} on ${on_string}: Scores for each allele in the database(s)" >
+<discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="scoresOutput" format="tabular"/>
+<filter>"save_scores" in output_files_selector</filter>
+</collection>
+<collection name="bowtie2_alignment_output" type="list" label="${tool.name} on ${on_string}: Bowtie2 alignment of reads to each input database" >
+<discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="bowtie2Alignments" format="bam"/>
+<filter>input['selector'] == "single" or input['selector'] == "paired"</filter>
+</collection>
+<collection name="samtools_pileup_alignment" type="list" label="${tool.name} on ${on_string}: Samtools pileup of the alignment to each input database" >
+<discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="samtoolsPileup" format="pileup"/>
+<filter>input['selector'] == "single" or input['selector'] == "paired"</filter>
+</collection>
+<data name="log_output" format="tabular" from_work_dir="output.log" label="${tool.name} on ${on_string}: Log file">
+<filter>"log" in output_files_selector</filter>
+</data>
+</outputs>
+<tests>
+<test expect_num_outputs="9">
+<param name="prob_err" value="0.01"/>
+<param name="max_unaligned_overlap" value="10"/>
+<param name="mapq" value="1"/>
+<param name="baseq" value="20"/>
+<param name="output_files_selector" value="log,save_scores,report_new_consensus,report_all_consensus"/>
+<conditional name="input">
+<param name="selector" value="paired"/>
+<param name="paired_input1" value="ERR024070_1_reduced_forward_reads.fastqsanger.gz"/>
+<param name="paired_input2" value="ERR024070_2_reduced_reverse_reads.fastqsanger.gz"/>
+<param name="merge_paired" value="false"/>
+<param name="read_type" value="q"/>
+</conditional>
+<conditional name="use_mlst_db">
+<param name="selector" value="yes"/>
+<param name="mlst_db" value="Escherichia_coli1R.fasta"/>
+<param name="mlst_definitions" value="profiles_csv"/>
+<param name="mlst_delimiter" value="_"/>
+<param name="mlst_max_mismatch" value="10"/>
+<param name="min_depth" value="5"/>
+<param name="min_edge_depth" value="2"/>
+</conditional>
+<conditional name="use_gene_db">
+<param name="selector" value="yes"/>
+<param name="gene_db" value="ARGannotR.fasta"/>
+<param name="no_gene_details" value="true"/>
+<param name="gene_max_mismatch" value="10"/>
+<param name="min_coverage" value="90"/>
+<param name="max_divergence" value="10"/>
+</conditional>
+<output name="mlst_results">
+<assert_contents>
+<has_text text="fumC"/>
+<has_n_lines n="2"/>
+</assert_contents>
+</output>
+<output_collection name="gene_typing" type="list">
+<element name="output__fullgenes__0-gene_db__results.txt">
+<assert_contents>
+<has_text text="AmpC1_Ecoli_Bla"/>
+<has_n_lines n="2"/>
+</assert_contents>
+</element>
+<element name="output__genes__0-gene_db__results.txt">
+<assert_contents>
+<has_text text="AmpC1_Ecoli_Bla"/>
+<has_n_lines n="2"/>
+</assert_contents>
+</element>
+</output_collection>
+<output name="Compiled_gene_and_mlst_output">
+<assert_contents>
+<has_text text="fumC"/>
+<has_n_lines n="2"/>
+</assert_contents>
+</output>
+<output name="all_consensus">
+<assert_contents>
+<has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
+<has_n_lines n="2"/>
+</assert_contents>
+</output>
+<output_collection name="new_consensus" type="list">
+<element name="49__AmpC1_Ecoli_Bla__AmpC1__1670.output__input.0-gene_db.pileup">
+<assert_contents>
+<has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
+<has_n_lines n="1196"/>
+</assert_contents>
+</element>
+</output_collection>
+<output_collection name="samtools_pileup_alignment" type="list">
+<element name="output__input.0-gene_db.pileup">
+<assert_contents>
+<has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
+<has_n_lines n="1196"/>
+</assert_contents>
+</element>
+</output_collection>
+<output_collection name="bowtie2_alignment_output" type="list">
+<element name="output__input.0-gene_db.sorted.bam">
+<assert_contents>
+<has_size value="18500" delta="1000"/>
+</assert_contents>
+</element>
+</output_collection>
+<output name="log_output">
+<assert_contents>
+<has_text text="Building"/>
+<has_n_lines n="52"/>
+</assert_contents>
+</output>
+</test>
+</tests>
+<help><![CDATA[
+SRST2
+=====
+Short Read Sequence Typing for Bacterial Pathogens
+This program is designed to take Illumina sequence data, a MLST (Multi Locus Sequence Types) database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs (Serotypes) and/or reference genes
+Read more about the tool: https://holtlab.net/2014/12/27/behind-the-paper-srst2-for-short-read-sequence-typing-of-bacterial-pathogens/
+Input
+=====
+Learn more about all inputs and their formates: https://github.com/katholt/srst2#input-read-formats-and-options
+Output
+======
+Learn more about all outputs: https://github.com/katholt/srst2#output-files
+]]></help>
+<citations>
+<citation type="doi">10.1186/s13073-014-0090-6</citation>
+</citations>
+</tool>

Mercurial > repos > iuc > srst2

comparison srst2.xml @ 0:36f105850c0d draft