comparison vsnp_sample_names.xml @ 3:fb3defef50e5 draft

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2:a56648c94fd3

<tool id="vsnp_sample_names" name="vSNP: sample names" version="1.0.0">
    <description></description>
    <command detect_errors="exit_code"><![CDATA[
#import os
#import re
#set output_dir = 'output'
mkdir -p $output_dir
#if str($input_type_cond.input_type) == "single":
    ## We may have a single read or a pair, but in
    ## either case we want the same base file name.
    #set sample_name = $os.path.basename($input_type_cond.read.element_identifier)
    #if $sample_name.find(".") > 0:
        #set sample_name = $sample_name.split(".")[0]
    #end if
    #if $sample_name.find("_") > 0:
        #set sample_name = $sample_name.split("_")[0]
    #end if
    && echo '$sample_name' > '$output'
#else:
    #for $i in $input_type_cond.reads_collection:
        #set sample_name = $os.path.basename($i.element_identifier)
        #if $sample_name.find(".") > 0:
            #set sample_name = $sample_name.split(".")[0]
        #end if
        #set output_file = $os.path.join($output_dir, $sample_name)
        && echo '$sample_name' > '$output_file'
    #end for
#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>
                <option value="collection">Collections of files</option>
            </param>
            <when value="single">
                <param name="read" type="data" format="fastqsanger.gz,fastqsanger" label="Sample file"/>
            </when>
            <when value="collection">
                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Collection of sample files"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="txt">
            <filter>input_type_cond['input_type'] == 'single'</filter>
        </data>
        <collection name="output__collection" type="list">
            <discover_datasets pattern="__name__" directory="output" format="txt" />
            <filter>input_type_cond['input_type'] == 'collection'</filter>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input_type" value="collection"/>
            <param name="reads_collection">
                <collection type="list">
                    <element name="BCG_Danish_Human_UK_SRR9596061.fastq" value="BCG_Danish_Human_UK_SRR9596061.fastq" dbkey="89"/>
                    <element name="Dassie_Dassie_ZA_SRR3745455.fastq" value="Dassie_Dassie_ZA_SRR3745455.fastq" dbkey="89"/>
                    <element name="Mbov_Cattle_NI_SRR10993937.fastq" value="Mbov_Cattle_NI_SRR10993937.fastq" dbkey="89"/>
                </collection>
            </param>
            <output_collection name="output__collection" type="list">
                <element name="BCG_Danish_Human_UK_SRR9596061" file="BCG_Danish_Human_UK_SRR9596061" ftype="txt"/>
                <element name="Dassie_Dassie_ZA_SRR3745455" file="Dassie_Dassie_ZA_SRR3745455" ftype="txt"/>
                <element name="Mbov_Cattle_NI_SRR10993937" file="Mbov_Cattle_NI_SRR10993937" ftype="txt"/>
            </output_collection>
        </test>
    </tests>
    <help>
**What it does**

Accepts one or more sample files and extracts a unique portion of the file name as the content of the output file(s).  These
text files are then used as workflow parameter values for the Read Group Identifier parameter in the bwa-mem tool.

**Required Options**

 * **Choose the category of the 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) based on the selected option.
    </help>
    <citations>
        <citation type="bibtex">
            @misc{None,
            journal = {None},
            author = {1. Stuber T},
            title = {Manuscript in preparation},
            year = {None},
            url = {https://github.com/USDA-VS/vSNP},}
        </citation>
    </citations>
</tool>

3:fb3defef50e5

<tool id="vsnp_sample_names" name="vSNP: sample names" version="@WRAPPER_VERSION@.1" profile="@PROFILE@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command detect_errors="exit_code"><![CDATA[
#import os
#import re

#set sample_name_read2 = None

#if $input_type_cond.input_type in ['single', 'pair']:
    #set read1 = $input_type_cond.read1
    #set sample_name = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
#else:
    #set read1_filename = $input_type_cond.reads_collection['forward'].name
    #set sample_name = re.sub('[^\s\w\-]', '_', str($read1_filename))
#end if

#if $sample_name.find('_R1') >0:
    ## Something like CMC_20E1_R1.fastq.gz
    #set sample_name = $sample_name.split('_R1')[0]
#else if $sample_name.find(".") > 0:
    #if $read1.is_of_type('fastqsanger.gz'):
        ## Something like my_sample.fastq.gz
        #set sample_name = '.'.join($sample_name.split('.')[0:-2])
    #else:
        ## Something like my_sample.fastq
        #set sample_name = $os.path.splitext($sample_name)[0]
    #end if
#else if $sample_name.find("_") > 0:
    #if $read1.is_of_type('fastqsanger.gz'):
        ## Something like my_sample_fastq_gz
        #set sample_name = '_'.join($sample_name.split('_')[0:-2])
    #else:
        ## Something like my_sample_fastq
        #set sample_name = "_".join($sample_name.split("_")[0:-1])
    #end if
#end if
echo '$sample_name' > '$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 dataset</option>
                <option value="pair">Dataset pair</option>
                <option value="paired">List of dataset pairs</option>
            </param>
            <when value="single">
                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 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"/>
            </when>
            <when value="pair">
                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
                <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="txt"/>
    </outputs>
    <tests>
        <!-- Single files -->
        <test>
            <param name="input_type" value="single"/>
            <param name="read1" value="CMC_20E1_R1.fastq.gz" dbkey="89"/>
            <output name="output" file="sample_names.txt" ftype="txt"/>
        </test>
        <!-- Paired reads -->
        <test>
            <param name="input_type" value="paired"/>
            <param name="reads_collection">
                <collection type="paired">
                    <element name="forward" value="CMC_20E1_R1.fastq.gz"/>
                    <element name="reverse" value="CMC_20E1_R2.fastq.gz"/>
                </collection>
            </param>
            <output name="output" file="sample_names.txt" ftype="txt"/>
        </test>
        <!-- Paired reads in separate datasets -->
        <test>
            <param name="input_type" value="pair"/>
            <param name="read1" value="CMC_20E1_R1.fastq.gz" dbkey="89"/>
            <param name="read2" value="CMC_20E1_R2.fastq.gz" dbkey="89"/>
            <output name="output" file="sample_names.txt" ftype="txt"/>
        </test>
    </tests>
    <help>
**What it does**

Accepts fastqsanger sample files, extracts a unique portion of the file name as the sample name, and writes it to
the output.  The output text file can be consumed by the **Parse parameter value** expression tool to provide workflow
parameter values to the **Read group identifier (ID)** and the **Sample name identifier (SM)**  parameters in the
**Map with BWA-MEM** tool.
    </help>
    <expand macro="citations"/>
</tool>