comparison vsnp_statistics.xml @ 1:14e29f7d59ca draft

Uploaded

0:c21d338dbdc4

    <description></description>
    <requirements>
        <requirement type="package" version="0.5.1">humanize</requirement>
        <requirement type="package" version="1.16.5">numpy</requirement>
        <requirement type="package" version="0.25.3">pandas</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#import os
#import re
#set gzipped = 'false'
#set input_type = $input_type_cond.input_type
#set input_idxstats_dir = 'input_idxstats'
#set input_metrics_dir = 'input_metrics'
#set input_reads_dir = 'input_reads'
#set output_dir = 'output'
mkdir -p $input_idxstats_dir &&
mkdir -p $input_metrics_dir &&
mkdir -p $input_reads_dir &&
mkdir -p $output_dir &&
#if str($input_type) == "single":
    #set read_type_cond = $input_type_cond.read_type_cond
    #set read1 = $read_type_cond.read1
    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
    #if str($read_type_cond.read_type) == "single":

        #if $i.is_of_type('fastqsanger.gz'):
            #set gzipped = 'true'
        #end if
        #set filename = $i.file_name
        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s $filename $input_reads_dir/$identifier &&
    #end for
    #for $i in $input_type_cond.samtools_idxstats_collection:
        #set filename = $i.file_name
        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s $filename $input_idxstats_dir/$identifier &&
    #end for
    #for $i in $input_type_cond.azc_metrics_collection:
        #set dbkey = $i.metadata.dbkey
        #set filename = $i.file_name
        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s $filename $input_metrics_dir/$identifier &&
    #end for
#end if
python '$__tool_directory__/vsnp_statistics.py'
--processes $processes
--dbkey '$dbkey'
--gzipped '$gzipped'
#if str($input_type) == "single":
    #if str($read_type_cond.read_type) == "single":
        --read1 '${read1_identifier}'

        --read1 '${read1_identifier}'
        --read2 '${read2_identifier}'
    #end if
    --samtools_idxstats '$samtools_idxstats'
    --vsnp_azc '$vsnp_azc'
    --output '$output'
#end if
]]></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>

                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Collection of fastqsanger files"/>
                <param name="samtools_idxstats_collection" type="data_collection" format="tabular" collection_type="list" label="Collection of samtools idxstats files"/>
                <param name="azc_metrics_collection" type="data_collection" format="tabular" collection_type="list" label="Collection of vSNP zero-coverage metrics files"/>
            </when>
        </conditional>
        <param name="processes" type="integer" min="1" max="20" value="8" label="Number of processes for job splitting"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular">
            <filter>input_type_cond['input_type'] == 'single'</filter>
        </data>
        <collection name="output_collection" type="list">
            <discover_datasets pattern="__name__" directory="output" format="tabular" />
            <filter>input_type_cond['input_type'] == 'collection'</filter>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
            <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
            <param name="samtools_idxstats" value="samtools_idxstats.tabular" ftype="tabular" dbkey="89"/>
            <param name="vsnp_azc" value="add_zc_metrics.tabular" ftype="tabular" dbkey="89"/>
            <output name="output" file="vsnp_statistics.tabular" ftype="tabular" compare="contains"/>
        </test>
    </tests>
    <help>
**What it does**

of coverage, good SNP count and more.

**Required options**

 * **Choose the type for files to be analyzed** - select "Single files" or "Collections of files", then select the appropriate history items (single or paired fastqsanger reads or collections of fastqsanger reads and associated idxstats and vSNP zero coverage metrics files) based on the selected option..
 * **Number of processes for job splitting** - Select the number of processes for splitting the job to shorten execution time.
    </help>
    <citations>
        <citation type="bibtex">
            @misc{None,
            journal = {None},

1:14e29f7d59ca

    <description></description>
    <requirements>
        <requirement type="package" version="0.5.1">humanize</requirement>
        <requirement type="package" version="1.16.5">numpy</requirement>
        <requirement type="package" version="0.25.3">pandas</requirement>
        <requirement type="package" version="1.2.0">xlrd</requirement>
        <requirement type="package" version="1.2.8">xlsxwriter</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#import os
#import re
#set gzipped = 'false'
#set input_type = $input_type_cond.input_type
#set input_idxstats_dir = 'input_idxstats'
#set input_metrics_dir = 'input_metrics'
#set input_reads_dir = 'input_reads'
mkdir -p $input_idxstats_dir &&
mkdir -p $input_metrics_dir &&
mkdir -p $input_reads_dir &&
#if str($input_type) == "single":
    #set read_type_cond = $input_type_cond.read_type_cond
    #set read1 = $read_type_cond.read1
    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
    #if str($read_type_cond.read_type) == "single":

        #if $i.is_of_type('fastqsanger.gz'):
            #set gzipped = 'true'
        #end if
        #set filename = $i.file_name
        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s '$filename' '$input_reads_dir/$identifier' &&
    #end for
    #for $i in $input_type_cond.samtools_idxstats_collection:
        #set filename = $i.file_name
        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s '$filename' '$input_idxstats_dir/$identifier' &&
    #end for
    #for $i in $input_type_cond.azc_metrics_collection:
        #set dbkey = $i.metadata.dbkey
        #set filename = $i.file_name
        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s '$filename' '$input_metrics_dir/$identifier' &&
    #end for
#end if
python '$__tool_directory__/vsnp_statistics.py'
--dbkey '$dbkey'
--gzipped '$gzipped'
#if str($input_type) == "single":
    #if str($read_type_cond.read_type) == "single":
        --read1 '${read1_identifier}'

        --read1 '${read1_identifier}'
        --read2 '${read2_identifier}'
    #end if
    --samtools_idxstats '$samtools_idxstats'
    --vsnp_azc '$vsnp_azc'
#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>

                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Collection of fastqsanger files"/>
                <param name="samtools_idxstats_collection" type="data_collection" format="tabular" collection_type="list" label="Collection of samtools idxstats files"/>
                <param name="azc_metrics_collection" type="data_collection" format="tabular" collection_type="list" label="Collection of vSNP zero-coverage metrics files"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="xlsx"/>
    </outputs>
    <tests>
        <test>
            <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
            <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
            <param name="samtools_idxstats" value="samtools_idxstats.tabular" ftype="tabular" dbkey="89"/>
            <param name="vsnp_azc" value="add_zc_metrics.tabular" ftype="tabular" dbkey="89"/>
            <output name="output" file="vsnp_statistics.xlsx" ftype="xlsx" compare="sim_size"/>
        </test>
    </tests>
    <help>
**What it does**

of coverage, good SNP count and more.

**Required options**

 * **Choose the type for files to be analyzed** - select "Single files" or "Collections of files", then select the appropriate history items (single or paired fastqsanger reads or collections of fastqsanger reads and associated idxstats and vSNP zero coverage metrics files) based on the selected option..
    </help>
    <citations>
        <citation type="bibtex">
            @misc{None,
            journal = {None},