comparison read-it-and-keep.xml @ 1:1563b58905f4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 5fcc308928ab2417b7e40227b27a3955f227649d"

0:554aa2a63f04

<tool id="read_it_and_keep" name="Read It and Keep" version="@TOOL_VERSION@+galaxy0" profile="20.09">
    <macros>
        <token name="@FASTQ_FORMATS@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
        <token name="@TOOL_VERSION@">0.1.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">read-it-and-keep</requirement>
        <requirement type="package">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $ref_source.source == "history"
            ln -s '$ref_source.ref_fasta' ref${trim_reference}.fasta &&
        #elif $ref_source.source == "builtin"
            ln -s '$ref_source.ref_fasta_builtin.path' ref${trim_reference}.fasta &&
        #end if
        #if $trim_reference
            python '$__tool_directory__/trim_reference.py' ref${trim_reference}.fasta ref.fasta &&
        #end if
        #if $reads.read_type == "paired"
            ln -s '$reads.read1' read1.fastq &&
            ln -s '$reads.read2' read2.fastq &&
        #elif $reads.read_type == 'paired_collection'
            ln -s '$reads.paired_reads.forward' read1.fastq &&
            ln -s '$reads.paired_reads.reverse' read2.fastq &&
        #elif $reads.read_type == 'single'
            ln -s '$reads.single_read1' read1.fastq &&
        #end if
        readItAndKeep
            --tech $sequencing_tech
            --ref_fasta ref.fasta
            --min_map_length $adv.min_map_length
            --min_map_length_pc $adv.min_map_length_pc
            --reads1 read1.fastq
            #if $reads.read_type != "single"
                --reads2 read2.fastq
            #end if
            -o output
            #if $reads.read_type == 'single'
                && mv output.reads.fastq.gz output.reads_1.fastq.gz
            #end if
    ]]></command>
    <inputs>
        <conditional name="reads">
            <param type="select" label="Read type" name="read_type">
                <option value="paired" selected="true">Paired end</option>
                <option value="paired_collection">Paired collection</option>
                <option value="single">Single ended</option>
            </param>
            <when value="paired">
                <param type="data" format="@FASTQ_FORMATS@" name="read1" label="Read1" />
                <param type="data" format="@FASTQ_FORMATS@" name="read2" label="Read2" />
            </when>
            <when value="paired_collection">
                <param type="data_collection" collection_type="paired" format="@FASTQ_FORMATS@" name="paired_reads" label="Reads" />
            </when>
            <when value="single">
                <param type="data" format="@FASTQ_FORMATS@" name="single_read1" label="Read1" />
            </when>
        </conditional>
        <conditional name="ref_source">
            <param type="select" label="Reference genome source" name="source">
                <option value="history" selected="true">History</option>

            <option value="ont">Oxford Nanopore</option>
        </param>
        <section name="adv" title="Advanced options">
            <param argument="--min_map_length" type="integer" min="0" value="50" label="Shortest match required to keep a read (in bp)" />
            <param argument="--min_map_length_pc" type="float" min="0.0" max="100.0" value="50.0" label="Minimum length of match required to keep a read (as percentage of read length" />
        </section>
    </inputs>
    <outputs>
        <data name="output_reads1" format="fastqsanger.gz" label="Filtered reads ${on_string} - reads1" from_work_dir="output.reads_1.fastq.gz">
            <filter>reads["read_type"] == "single" or reads["read_type"] == "paired"</filter>
        </data>
        <data name="output_reads2" format="fastqsanger.gz" label="Filtered reads ${on_string} - reads2" from_work_dir="output.reads_2.fastq.gz">
            <filter>reads["read_type"] == "paired"</filter>
        </data>
        <collection type="paired" format="fastqsanger.gz" name="output_collection" label="Filtered reads ${on_string}">
            <filter>reads["read_type"] == "paired_collection"</filter>
            <data name="forward" format="fastqsanger.gz" from_work_dir="output.reads_1.fastq.gz" />
            <data name="reverse" format="fastqsanger.gz" from_work_dir="output.reads_2.fastq.gz" />
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <conditional name="reads">
                <param name="read_type" value="paired" />
                <param name="read1" value="test1.fastq.gz" ftype="fastqsanger.gz" />
                <param name="read2" value="test2.fastq.gz" ftype="fastqsanger.gz" />

            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="illumina" />
            <output name="output_reads1" value="output_test1.fastq.gz" />
            <output name="output_reads2" value="output_test2.fastq.gz" />
        </test>
        <test expect_num_outputs="3">
            <conditional name="reads">
                <param name="read_type" value="paired_collection" />
                <param name="paired_reads">
                    <collection type="paired">
                        <element name="forward" value="test1.fastq.gz" ftype="fastqsanger.gz" />
                        <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger.gz" />    
                    </collection>
                </param>
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="illumina" />
            <output_collection name="output_collection">
                <element name="forward" value="output_test1.fastq.gz" />
                <element name="reverse" value="output_test2.fastq.gz" />
            </output_collection>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reads">
                <param name="read_type" value="single" />
                <param name="single_read1" value="test3.fastq.gz" ftype="fastqsanger.gz"/>
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="ont" />
            <output name="output_reads1" value="output_test3.fastq.gz" />
        </test>
    </tests>
    <help><![CDATA[
ReadItAndKeep
-------------

1:1563b58905f4

<tool id="read_it_and_keep" name="Read It and Keep" version="@TOOL_VERSION@+galaxy0" profile="20.09">
    <macros>
        <token name="@INPUT_FORMATS@">fasta,fastq,fasta.gz,fastq.gz</token>
        <token name="@TOOL_VERSION@">0.2.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">read-it-and-keep</requirement>
        <requirement type="package" version="3.10">python</requirement>
    </requirements>
    <version_command><![CDATA[readItAndKeep -V]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
        #if $ref_source.source == "history"
            ln -s '$ref_source.ref_fasta' ref${trim_reference}.fasta &&
        #elif $ref_source.source == "builtin"
            ln -s '$ref_source.ref_fasta_builtin.path' ref${trim_reference}.fasta &&
        #end if
        #if $trim_reference
            python '$__tool_directory__/trim_reference.py' ref${trim_reference}.fasta ref.fasta &&
        #end if
        #if $reads.read_type == "paired"
            #set $ext_out1 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq'
            #set $ext_out2 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq'
            ln -s '$reads.read1' read1 &&
            ln -s '$reads.read2' read2 &&
        #elif $reads.read_type == 'paired_collection'
        #set $ext_out1 = 'fasta' if $reads.paired_reads.forward.ext in ['fasta', 'fasta.gz'] else 'fastq'
            #set $ext_out2 = 'fasta' if $reads.paired_reads.reverse.ext in ['fasta', 'fasta.gz'] else 'fastq'
            ln -s '$reads.paired_reads.forward' read1 &&
            ln -s '$reads.paired_reads.reverse' read2 &&
        #elif $reads.read_type == 'single'
            #set $ext_out1 = 'fasta' if $reads.read1.ext in ['fasta', 'fasta.gz'] else 'fastq'
            ln -s '$reads.read1' read1 &&
        #end if
        readItAndKeep
            --tech $sequencing_tech
            --ref_fasta ref.fasta
            --min_map_length $adv.min_map_length
            --min_map_length_pc $adv.min_map_length_pc
            $adv.enumerate_names
            --reads1 read1
            #if $reads.read_type != "single"
                --reads2 read2
            #end if
            -o output
            #if $reads.read_type == 'single':
                && mv output.reads.${ext_out1}.gz output.reads_1.${ext_out1}.gz
            #end if
            #if $reads.read_type == 'paired_collection':
                #if not $reads.paired_reads.forward.ext.endswith('.gz'):
                    && gunzip ./output.reads_1.${ext_out1}.gz
                    && gunzip ./output.reads_2.${ext_out2}.gz
                #end if
            #elif not $reads.read1.ext.endswith('.gz'):
                && gunzip ./output.reads_1.${ext_out1}.gz
                #if $reads.read_type != 'single' and not $reads.read2.ext.endswith('.gz'):
                    && gunzip ./output.reads_2.${ext_out2}.gz
                #end if
            #end if
    ]]></command>
    <inputs>
        <conditional name="reads">
            <param type="select" label="Read type" name="read_type">
                <option value="paired" selected="true">Paired end</option>
                <option value="paired_collection">Paired collection</option>
                <option value="single">Single ended</option>
            </param>
            <when value="paired">
                <param type="data" format="@INPUT_FORMATS@" name="read1" label="Read1" />
                <param type="data" format="@INPUT_FORMATS@" name="read2" label="Read2" />
            </when>
            <when value="paired_collection">
                <param type="data_collection" collection_type="paired" format="@INPUT_FORMATS@" name="paired_reads" label="Reads" />
            </when>
            <when value="single">
                <param type="data" format="@INPUT_FORMATS@" name="read1" label="Read1" />
            </when>
        </conditional>
        <conditional name="ref_source">
            <param type="select" label="Reference genome source" name="source">
                <option value="history" selected="true">History</option>

            <option value="ont">Oxford Nanopore</option>
        </param>
        <section name="adv" title="Advanced options">
            <param argument="--min_map_length" type="integer" min="0" value="50" label="Shortest match required to keep a read (in bp)" />
            <param argument="--min_map_length_pc" type="float" min="0.0" max="100.0" value="50.0" label="Minimum length of match required to keep a read (as percentage of read length" />
            <param name="enumerate_names" type="boolean" truevalue="--enumerate_names" falsevalue="" label="Rename the reads 1,2,3,... (for paired reads, will also add /1 or /2 to the end of names)" />
        </section>
    </inputs>
    <outputs>
        <data name="output_reads1" format_source="read1" label="Filtered reads ${on_string} - reads1" from_work_dir="output.reads_1.fast*">
            <filter>reads["read_type"] == "single" or reads["read_type"] == "paired"</filter>
        </data>
        <data name="output_reads2" format_source="read2" label="Filtered reads ${on_string} - reads2" from_work_dir="output.reads_2.fast*">
            <filter>reads["read_type"] == "paired"</filter>
        </data>
        <collection type="paired" name="output_collection" format_source="paired_reads" label="Filtered reads ${on_string}">
            <filter>reads["read_type"] == "paired_collection"</filter>
            <data name="forward" from_work_dir="output.reads_1.fast*" />
            <data name="reverse" from_work_dir="output.reads_2.fast*" />
        </collection>
    </outputs>
    <tests>
        <!--Testing uncompressed fastq input-->
        <test expect_num_outputs="2">
            <conditional name="reads">
                <param name="read_type" value="paired" />
                <param name="read1" value="test1.fastq.gz" ftype="fastqsanger" />
                <param name="read2" value="test2.fastq.gz" ftype="fastqsanger" />
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="illumina" />
            <output name="output_reads1" file="output.test1.reads_1.fastq" ftype="fastqsanger"/>
            <output name="output_reads2" file="output.test1.reads_2.fastq" ftype="fastqsanger"/>
        </test>
        <test expect_num_outputs="3">
            <conditional name="reads">
                <param name="read_type" value="paired_collection" />
                <param name="paired_reads">
                    <collection type="paired">
                        <element name="forward" value="test1.fastq.gz" ftype="fastqsanger" />
                        <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger" />
                    </collection>
                </param>
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="illumina" />
            <output_collection name="output_collection" type="paired">
                <element name="forward" file="output.test1.reads_1.fastq" ftype="fastqsanger"/>
                <element name="reverse" file="output.test1.reads_2.fastq" ftype="fastqsanger"/>
            </output_collection>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reads">
                <param name="read_type" value="single" />
                <param name="read1" value="test3.fastq.gz" ftype="fastqsanger"/>
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="ont" />
            <param name="enumerate_names" value="True" />
            <output name="output_reads1" file="output.test3.reads_1.fastq" ftype="fastqsanger"/>
        </test>
        <!--Testing uncompressed fasta input-->
        <test expect_num_outputs="2">
            <conditional name="reads">
                <param name="read_type" value="paired" />
                <param name="read1" value="test1.fasta.gz" ftype="fasta" />
                <param name="read2" value="test2.fasta.gz" ftype="fasta" />
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="illumina" />
            <output name="output_reads1" file="output.test1.reads_1.fasta" ftype="fasta"/>
            <output name="output_reads2" file="output.test1.reads_2.fasta" ftype="fasta"/>
        </test>
        <test expect_num_outputs="3">
            <conditional name="reads">
                <param name="read_type" value="paired_collection" />
                <param name="paired_reads">
                    <collection type="paired">
                        <element name="forward" value="test1.fasta.gz" ftype="fasta" />
                        <element name="reverse" value="test2.fasta.gz" ftype="fasta" />
                    </collection>
                </param>
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="illumina" />
            <output_collection name="output_collection" type="paired">
                <element name="forward" file="output.test1.reads_1.fasta" ftype="fasta"/>
                <element name="reverse" file="output.test1.reads_2.fasta" ftype="fasta"/>
            </output_collection>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reads">
                <param name="read_type" value="single" />
                <param name="read1" value="test3.fasta.gz" ftype="fasta"/>
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="ont" />
            <param name="enumerate_names" value="True" />
            <output name="output_reads1" file="output.test3.reads_1.fasta" ftype="fasta"/>
        </test>
        <!--Testing compressed fasta input-->
        <test expect_num_outputs="2">
            <conditional name="reads">
                <param name="read_type" value="paired" />
                <param name="read1" value="test1.fasta.gz" ftype="fasta.gz" />
                <param name="read2" value="test2.fasta.gz" ftype="fasta.gz" />
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="illumina" />
            <output name="output_reads1" decompress="true" file="output.test1.reads_1.fasta" ftype="fasta.gz"/>
            <output name="output_reads2" decompress="true" file="output.test1.reads_2.fasta" ftype="fasta.gz"/>
        </test>
        <test expect_num_outputs="3">
            <conditional name="reads">
                <param name="read_type" value="paired_collection" />
                <param name="paired_reads">
                    <collection type="paired">
                        <element name="forward" value="test1.fasta.gz" ftype="fasta.gz" />
                        <element name="reverse" value="test2.fasta.gz" ftype="fasta.gz" />
                    </collection>
                </param>
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="illumina" />
            <output_collection name="output_collection" type="paired">
                <element name="forward" ftype="fasta.gz">
                    <assert_contents>
                        <has_size value="680" delta="50" />
                    </assert_contents>
                </element>
                <element name="reverse" ftype="fasta.gz">
                    <assert_contents>
                        <has_size value="670" delta="50" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reads">
                <param name="read_type" value="single" />
                <param name="read1" value="test3.fasta.gz" ftype="fasta.gz"/>
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="ont" />
            <param name="enumerate_names" value="True" />
            <output name="output_reads1" decompress="true" file="output.test3.reads_1.fasta" ftype="fasta.gz"/>
        </test>
        <!--Testing compressed fastq input-->
        <test expect_num_outputs="2">
            <conditional name="reads">
                <param name="read_type" value="paired" />
                <param name="read1" value="test1.fastq.gz" ftype="fastqsanger.gz" />
                <param name="read2" value="test2.fastq.gz" ftype="fastqsanger.gz" />

            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="illumina" />
            <output name="output_reads1" decompress="true" file="output.test1.reads_1.fastq" ftype="fastqsanger.gz"/>
            <output name="output_reads2" decompress="true" file="output.test1.reads_2.fastq" ftype="fastqsanger.gz"/>
        </test>
        <test expect_num_outputs="3">
            <conditional name="reads">
                <param name="read_type" value="paired_collection" />
                <param name="paired_reads">
                    <collection type="paired">
                        <element name="forward" value="test1.fastq.gz" ftype="fastqsanger.gz" />
                        <element name="reverse" value="test2.fastq.gz" ftype="fastqsanger.gz" />
                    </collection>
                </param>
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="illumina" />
            <output_collection name="output_collection" type="paired">
                <element name="forward" ftype="fastqsanger.gz">
                    <assert_contents>
                        <has_size value="995" delta="50" />
                    </assert_contents>
                </element>
                <element name="reverse" ftype="fastqsanger.gz">
                    <assert_contents>
                        <has_size value="960" delta="50" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="1">
            <conditional name="reads">
                <param name="read_type" value="single" />
                <param name="read1" value="test3.fastq.gz" ftype="fastqsanger.gz"/>
            </conditional>
            <conditional name="ref_source">
                <param name="source" value="history" />
                <param name="ref_fasta" value="reference.fasta" ftype="fasta" />
            </conditional>
            <param name="sequencing_tech" value="ont" />
            <param name="enumerate_names" value="True" />
            <output name="output_reads1" decompress="true" file="output.test3.reads_1.fastq" ftype="fastqsanger.gz"/>
        </test>
    </tests>
    <help><![CDATA[
ReadItAndKeep
-------------