comparison bowtie2_wrapper.xml @ 10:a9d4f71dbfb0 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d

9:019c2a81547a

<tool id="bowtie2" name="Bowtie2" version="2.2.6">
    <description>- map reads against reference genome</description>
    <macros>
        <import>read_group_macros.xml</import>
    </macros>
    <version_command>bowtie2 --version</version_command>
    <requirements>
        <requirement type="package" version="2.2.6">bowtie2</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <command>

        ## prepare bowtie2 index
        #set index_path = ''
        #if str($reference_genome.source) == "history":
            bowtie2-build "$reference_genome.own_file" genome &amp;&amp;
            ln -s "$reference_genome.own_file" genome.fa &amp;&amp;

        ## Fastq inputs
        #if str( $library.type ) == "single":
            -U "${library.input_1}"
            #if str( $library.unaligned_file ) == "true":
                --un $output_unaligned_reads_l
            #end if
        #elif str( $library.type ) == "paired":
            -1 "${library.input_1}"
            -2 "${library.input_2}"
            #if str( $library.paired_options.paired_options_selector ) == "yes":

                ${library.paired_options.no_contain}
                ${library.paired_options.no_overlap}
            #end if
            #if str( $library.unaligned_file ) == "true":
                --un-conc $output_unaligned_reads_l
            #end if
        #else
            ## prepare collection
            -1 $library.input_1.forward
            -2 $library.input_1.reverse

        #elif str( $analysis_type.analysis_type_selector ) == "cline":
            ${analysis_type.cline}
        #end if

        ## output file
        #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
          | samtools view -Su - | samtools sort -o - - > $output
        #else
          > $output_sam

        #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
            #from os.path import splitext
            #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
            && mv "${ _unaligned_root }.1${_unaligned_ext}" "${ output_unaligned_reads_l }"
            && mv "${ _unaligned_root }.2${_unaligned_ext}" "${ output_unaligned_reads_r }"
        #end if

    </command>
    <!-- basic error handling -->
    <stdio>

            </param>

            <when value="single">
                <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
            </when>
            <when value="paired">
                <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
                <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
                <conditional name="paired_options">
                    <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
                        <option value="no" selected="True">No</option>
                        <option value="yes">Yes</option>
                    </param>

                </conditional>
            </when>
            <when value="paired_collection">
                <param name="input_1" format="fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot;" />
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
                <conditional name="paired_options">
                    <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
                        <option value="no" selected="True">No</option>
                        <option value="yes">Yes</option>
                    </param>

                    </when>
                </conditional>
                <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
            </when>
        </conditional>
    </inputs>

    <!-- define outputs -->
    
    <outputs>

                        </action>
                    </when>
                    <when value="paired_collection">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>

                  <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
                </action>
              </when>
            </conditional>
          </actions>
        </data>

    </outputs>

    <tests>

            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
        </test>
    </tests>

    <help>
        
**Bowtie2 Overview**

10:a9d4f71dbfb0

<tool id="bowtie2" name="Bowtie2" version="2.2.6.2">
    <description>- map reads against reference genome</description>
    <macros>
        <import>read_group_macros.xml</import>
    </macros>
    <version_command>bowtie2 --version</version_command>
    <requirements>
        <requirement type="package" version="2.2.6">bowtie2</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <command>
        ## prepare bowtie2 index
        #set index_path = ''
        #if str($reference_genome.source) == "history":
            bowtie2-build "$reference_genome.own_file" genome &amp;&amp;
            ln -s "$reference_genome.own_file" genome.fa &amp;&amp;

        ## Fastq inputs
        #if str( $library.type ) == "single":
            -U "${library.input_1}"
            #if str( $library.unaligned_file ) == "true":
                --un $output_unaligned_reads_l
            #end if
            #if str( $library.aligned_file ) == "true":
                --al $output_aligned_reads_l
            #end if
        #elif str( $library.type ) == "paired":
            -1 "${library.input_1}"
            -2 "${library.input_2}"
            #if str( $library.paired_options.paired_options_selector ) == "yes":

                ${library.paired_options.no_contain}
                ${library.paired_options.no_overlap}
            #end if
            #if str( $library.unaligned_file ) == "true":
                --un-conc $output_unaligned_reads_l
            #end if
            #if str( $library.aligned_file ) == "true":
                --al-conc $output_aligned_reads_l
            #end if
        #else
            ## prepare collection
            -1 $library.input_1.forward
            -2 $library.input_1.reverse

        #elif str( $analysis_type.analysis_type_selector ) == "cline":
            ${analysis_type.cline}
        #end if

        ## mapping stats (i.e. stderr from bowtie2)
        #if $save_mapping_stats
	  2> "$mapping_stats"
        #end if

        ## output file
        #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
          | samtools view -Su - | samtools sort -o - - > $output
        #else
          > $output_sam

        #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
            #from os.path import splitext
            #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
            && mv "${ _unaligned_root }.1${_unaligned_ext}" "${ output_unaligned_reads_l }"
            && mv "${ _unaligned_root }.2${_unaligned_ext}" "${ output_unaligned_reads_r }"
        #end if
        #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
            #from os.path import splitext
            #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
            && mv "${ _aligned_root }.1${_aligned_ext}" "${ output_aligned_reads_l }"
            && mv "${ _aligned_root }.2${_aligned_ext}" "${ output_aligned_reads_r }"
        #end if

    </command>
    <!-- basic error handling -->
    <stdio>

            </param>

            <when value="single">
                <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
                <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc; This triggers --al parameter for single reads and --al-conc for paired reads" />
            </when>
            <when value="paired">
                <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
                <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
                <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc; This triggers --al parameter for single reads and --al-conc for paired reads" />
                <conditional name="paired_options">
                    <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
                        <option value="no" selected="True">No</option>
                        <option value="yes">Yes</option>
                    </param>

                </conditional>
            </when>
            <when value="paired_collection">
                <param name="input_1" format="fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot;" />
                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
                <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc; This triggers --al parameter for single reads and --al-conc for paired reads" />
                <conditional name="paired_options">
                    <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
                        <option value="no" selected="True">No</option>
                        <option value="yes">Yes</option>
                    </param>

                    </when>
                </conditional>
                <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
            </when>
        </conditional>
        <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
    </inputs>

    <!-- define outputs -->
    
    <outputs>

                        </action>
                    </when>
                    <when value="paired_collection">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
        <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
            <filter>library['aligned_file'] is True</filter>
            <actions>
                <conditional name="library.type">
                    <when value="single">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired_collection">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
        <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
            <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
            <actions>
                <conditional name="library.type">
                    <when value="paired">
                        <action type="format">
                            <option type="from_param" name="library.input_2" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired_collection">
                        <action type="format">
                            <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>

                  <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
                </action>
              </when>
            </conditional>
          </actions>
        </data>
        <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
          <filter>save_mapping_stats is True</filter>
        </data>

    </outputs>

    <tests>

            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <!-- basic test on single paired default run with stats-->
            <param name="type" value="paired"/>
            <param name="selection" value="no"/>
            <param name="paired_options_selector" value="no"/>
            <param name="unaligned_file" value="false"/>
            <param name="analysis_type_selector" value="simple"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <param name="save_mapping_stats" value="true" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
            <output name="mapping_stats" file="bowtie2-stats.out" ftype="txt"/>
        </test>
    </tests>

    <help>
        
**Bowtie2 Overview**