comparison srst2.xml @ 1:599a4dc309aa draft

planemo upload commit 1ea98fb88a93a571beda5bbd56449c946860a258

0:6f870ed59b6e

<tool id="srst2" name="SRST2" version="0.3.6">
    <description>Short Read Sequence Typing for Bacterial Pathogens</description>
    <requirements>
        <requirement type="package" version="0.1.18">samtools</requirement>
        <requirement type="package" version="2.1.0">bowtie2</requirement>
        <requirement type="package" version="0.1.4.6">srst2</requirement>
        <requirement type="package" version="08-07-2014">vfdb</requirement>
    </requirements>
    <stdio>
      <exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
    </stdio>
    <command interpreter="perl">
        srst2.pl \$BASE/srst2.py $bam_results $scores $pileup

        #if $mlst_or_genedb.job_type == "mlst_only"
            m $txt_results $alleles
            #if ($mlst_or_genedb.allele_choice.allele_report=="all")
                all
            #else if ($mlst_or_genedb.allele_choice.allele_report=="new")
                new
            #end if
        #else if $mlst_or_genedb.job_type == "custom_only"
            g $genes_results $fullgenes_results
    #*
    to allow multiple custom databases join all db names into comma separated variable then send that variable to the perl script to be parsed
    make the database names an array and then join
    *#
            #set $dbs = ','.join([$database.gene_db.name for $database in ( $mlst_or_genedb.databases )])
            "$dbs"
        #else if $mlst_or_genedb.job_type == "vfdb_only"
            g $genes_results $fullgenes_results $mlst_or_genedb.vfdb_in.name
        #else if $mlst_or_genedb.job_type == "mlst_custom"

            #end if
        #else
            --other "'-p \${GALAXY_SLOTS:-1}'"
        #end if

        --output out
    </command>
    <inputs>
        <conditional name="single_or_paired">
            <param name="type" type="select" label="Read type">
                <option value="single">Single-end</option>
                <option value="paired">Paired-end</option>
                <option value="collection">Collection Paired-end</option>
                </param>
            <when value="single">
                <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
            </when>
            <when value="paired">
                <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
                <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
            </when>
            <when value="collection">
                <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="txt" collection_type="paired" />
            </when>
        </conditional>

        <conditional name="mlst_or_genedb">
            <param name="job_type" type="select" label="Job type">

            </when>
            <when value="mlst_vfdb">
                <param name="mlst_defs" type="data" format="tabular"  label="ST definitions for MLST scheme"/>
                <param name="mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/>
                <param name="vfdb_in" type="select" label="Choose a VFDB strain">
                <options from_data_table="vfdb_fasta_files" />
                </param>
                <param name="mlst_max_mismatch" type="integer" label="Maximum number of mismatches per read for MLST allele calling" value=""  help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/>
                <param name="gene_max_mismatch" type="integer" label="Maximum number of mismatches per read for gene allele calling" value=""  help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/>
                <param name="mlst_delim" type="text" label="Character(s) separating gene name from allele number in MLST database" value="" help="Typically _ or -" optional="false" >
                    <validator type="expression" message="Must enter a delimiter.">len(value) >= 1</validator>

            <filter>mlst_or_genedb['job_type']!= "mlst_only"</filter>
        </data>
    </outputs>

    <tests>
      <test>
        <output/>
      </test>
    </tests>


    <help>
What it does

    Philip Mabon

    Mark Iskander

    </help>
    <citations>
      <citation type="doi">10.1128/AAC.01310-13</citation>
    </citations>
</tool>

1:599a4dc309aa

<tool id="srst2" name="SRST2" version="0.3.7">
    <description>Short Read Sequence Typing for Bacterial Pathogens</description>
    <requirements>
        <requirement type="package" version="0.1.4.6">srst2</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
    </stdio>
    <command><![CDATA[
        $__tool_directory__/srst2.pl $bam_results $scores $pileup

        #if $mlst_or_genedb.job_type == "mlst_only"
            m $txt_results $alleles
            #if ($mlst_or_genedb.allele_choice.allele_report=="all")
                all
            #else if ($mlst_or_genedb.allele_choice.allele_report=="new")
                new
            #end if
        #else if $mlst_or_genedb.job_type == "custom_only"
            g $genes_results $fullgenes_results
            #*
            to allow multiple custom databases join all db names into comma separated variable then send that variable to the perl script to be parsed
            make the database names an array and then join
            *#
            #set $dbs = ','.join([$database.gene_db.name for $database in ( $mlst_or_genedb.databases )])
            "$dbs"
        #else if $mlst_or_genedb.job_type == "vfdb_only"
            g $genes_results $fullgenes_results $mlst_or_genedb.vfdb_in.name
        #else if $mlst_or_genedb.job_type == "mlst_custom"

            #end if
        #else
            --other "'-p \${GALAXY_SLOTS:-1}'"
        #end if

        --output \${PWD}/out
    ]]></command>
    <inputs>
        <conditional name="single_or_paired">
            <param name="type" type="select" label="Read type">
                <option value="single">Single-end</option>
                <option value="paired">Paired-end</option>
                <option value="collection">Collection Paired-end</option>
            </param>
            <when value="single">
                <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
            </when>
            <when value="paired">
                <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
                <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
            </when>
            <when value="collection">
                <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
            </when>
        </conditional>

        <conditional name="mlst_or_genedb">
            <param name="job_type" type="select" label="Job type">

            </when>
            <when value="mlst_vfdb">
                <param name="mlst_defs" type="data" format="tabular"  label="ST definitions for MLST scheme"/>
                <param name="mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/>
                <param name="vfdb_in" type="select" label="Choose a VFDB strain">
                    <options from_data_table="vfdb_fasta_files" />
                </param>
                <param name="mlst_max_mismatch" type="integer" label="Maximum number of mismatches per read for MLST allele calling" value=""  help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/>
                <param name="gene_max_mismatch" type="integer" label="Maximum number of mismatches per read for gene allele calling" value=""  help="SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls."/>
                <param name="mlst_delim" type="text" label="Character(s) separating gene name from allele number in MLST database" value="" help="Typically _ or -" optional="false" >
                    <validator type="expression" message="Must enter a delimiter.">len(value) >= 1</validator>

            <filter>mlst_or_genedb['job_type']!= "mlst_only"</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="type" value="collection" />
            <param name="fastq_collection">
                <collection type="paired">
                    <element name="forward" value="ERR028678_sampled_1.fastq" />
                    <element name="reverse" value="ERR028678_sampled_2.fastq" />
                </collection>
            </param>
            <param name="job_type" value="mlst_only" />
            <param name="mlst_defs" value="ecoli.txt" />
            <param name="mlst_db" value="Escherichia_coli#1.fasta" />
            <param name="mlst_max_mismatch" value="10" />
            <param name="mlst_delim" value="-" />
            <output name="bam_results" file="ERR028678_sampled.bam" ftype="bam" lines_diff="2" />
            <output name="scores" file="ERR028678_sampled_scores.tabular" />
            <!-- Don't test pileup as it is too large of a file > 90 MB -->
            <!-- <output name="pileup" file="ERR028678_sampled_pileup.tabular" />-->
            <output name="alleles" file="ERR028678_sampled_alleles.fasta" />
            <output name="txt_results" file="ERR028678_sampled_text_results.tabular" />
        </test>
    </tests>


    <help>
What it does

    Philip Mabon

    Mark Iskander

    Eric Enns

    </help>
    <citations>
      <citation type="doi">10.1128/AAC.01310-13</citation>
    </citations>
</tool>