view vsnp_statistics.xml @ 4:a2f69b1598e0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3

<tool id="vsnp_statistics" name="vSNP: statistics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command detect_errors="exit_code"><![CDATA[
#import re

#if $input_type_cond.input_type in ["single", "pair"]:
    #set read1 = $input_type_cond.read1
    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
    ln -s '${read1}' '${read1_identifier}' &&
    #set read1_seqkit_stats = $input_type_cond.read1_seqkit_stats
    #set read1_seqkit_fx2tab = $input_type_cond.read1_seqkit_fx2tab
    #if $input_type_cond.input_type == "pair":
        #set read2 = $input_type_cond.read2
        #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
        ln -s '${read2}' '${read2_identifier}' &&
        #set read2_seqkit_stats = $input_type_cond.read2_seqkit_stats
        #set read2_seqkit_fx2tab = $input_type_cond.read2_seqkit_fx2tab
    #end if
#else:
    #set identifier = re.sub('[^\s\w\-]', '_', str($input_type_cond.reads_collection.element_identifier))
    #set read1 = $input_type_cond.reads_collection.forward
    #set read1_identifier = $identifier + '_R1'
    ln -s '${read1}' '${read1_identifier}' &&
    #set read2 = $input_type_cond.reads_collection.reverse
    #set read2_identifier = $identifier + '_R2'
    ln -s '${read2}' '${read2_identifier}' &&
    #set identifier = re.sub('[^\s\w\-]', '_', str($input_type_cond.seqkit_stats_collection.element_identifier))
    #set read1_seqkit_stats = $input_type_cond.seqkit_stats_collection.forward
    #set read2_seqkit_stats = $input_type_cond.seqkit_stats_collection.reverse
    #set identifier = re.sub('[^\s\w\-]', '_', str($input_type_cond.seqkit_fx2tab_collection.element_identifier))
    #set read1_seqkit_fx2tab = $input_type_cond.seqkit_fx2tab_collection.forward
    #set read2_seqkit_fx2tab = $input_type_cond.seqkit_fx2tab_collection.reverse
#end if

python '$__tool_directory__/vsnp_statistics.py'
--read1 '${read1_identifier}'
--read1_seqkit_stats '$read1_seqkit_stats'
--read1_seqkit_fx2tab '$read1_seqkit_fx2tab'
#if $input_type_cond.input_type in ['pair', 'paired']:
    --read2 '${read2_identifier}'
    --read2_seqkit_stats '$read2_seqkit_stats'
    --read2_seqkit_fx2tab '$read2_seqkit_fx2tab'
#end if
--output '$output'
]]></command>
    <inputs>
        <conditional name="input_type_cond">
            <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
                <option value="single" selected="true">Single files</option>
                <option value="paired">Paired reads</option>
                <option value="pair">Paired reads in separate data sets</option>
            </param>
            <when value="single">
                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Fastq file"/>
                <param name="read1_seqkit_stats" type="data" format="tabular" label="SeqKit statistics file for selected Fastq file"/>
                <param name="read1_seqkit_fx2tab" type="data" format="tabular" label="SeqKit fx2tab file for selected Fastq file"/>
            </when>
            <when value="paired">
                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
                <param name="seqkit_stats_collection" type="data_collection" format="tabular" collection_type="paired" label="Collection of paired SeqKit statistics files"/>
                <param name="seqkit_fx2tab_collection" type="data_collection" format="tabular" collection_type="paired" label="Collection of paired SeqKit fx2tab files"/>
            </when>
            <when value="pair">
                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward read fastq file"/>
                <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse read fastq file"/>
                <param name="read1_seqkit_stats" type="data" format="tabular" label="SeqKit statistics file for selected forward read"/>
                <param name="read2_seqkit_stats" type="data" format="tabular" label="SeqKit statistics file for selected reverse read"/>
                <param name="read1_seqkit_fx2tab" type="data" format="tabular" label="SeqKit fx2tab file for selected forward read"/>
                <param name="read2_seqkit_fx2tab" type="data" format="tabular" label="SeqKit fx2tab file for selected reverse read"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <!-- A single fastq file -->
        <test expect_num_outputs="1">
            <param name="input_type" value="single"/>
            <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="read1_seqkit_stats" value="r1_seqkit_stats1.tabular" ftype="tabular"/>
            <param name="read1_seqkit_fx2tab" value="r1_seqkit_fx2tab1.tabular" ftype="tabular"/>
            <output name="output" file="statistics_output1.tabular" ftype="tabular"/>
        </test>
        <!-- A set of paired fastq files -->
        <test expect_num_outputs="1">
            <param name="input_type" value="pair"/>
            <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="read1_seqkit_stats" value="r1_seqkit_stats2.tabular" ftype="tabular"/>
            <param name="read2_seqkit_stats" value="r2_seqkit_stats2.tabular" ftype="tabular"/>
            <param name="read1_seqkit_fx2tab" value="r1_seqkit_fx2tab2.tabular" ftype="tabular"/>
            <param name="read2_seqkit_fx2tab" value="r2_seqkit_fx2tab2.tabular" ftype="tabular"/>
            <output name="output" file="statistics_output2.tabular" ftype="tabular"/>
        </test>
        <!-- A collection of paired fastq files -->
        <test expect_num_outputs="1">
            <param name="input_type" value="paired"/>
            <param name="reads_collection">
                <collection type="paired">
                    <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
                    <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
                </collection>
            </param>
            <param name="seqkit_stats_collection">
                <collection type="paired">
                    <element name="forward" value="r1_seqkit_stats2.tabular" ftype="tabular"/>
                    <element name="reverse" value="r2_seqkit_stats2.tabular" ftype="tabular"/>
                </collection>
            </param>
            <param name="seqkit_fx2tab" value="seqkit_fx2tab3.tabular" ftype="tabular"/>
            <param name="seqkit_fx2tab_collection">
                <collection type="paired">
                    <element name="forward" value="r1_seqkit_fx2tab2.tabular" ftype="tabular"/>
                    <element name="reverse" value="r2_seqkit_fx2tab2.tabular" ftype="tabular"/>
                </collection>
            </param>
            <output name="output" file="statistics_output3.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>
**What it does**

Accepts fastq samples and SeqKit stats and fx2tab files produced from the samples and extracts information from them to produce a tabular
file containing statistics for each sample.  The samples can be a single read, a single set of paired reads in separate datasets or a
collection of paired reas.  The output statistics include file size, read count, sum / avg / max read length, Q1, Q2, Q3, sum gap, N50,
reads passing Q20 / Q30, and average read quality.
    </help>
    <expand macro="citations"/>
</tool>