comparison hisat2.xml @ 7:5ba8e317529a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde

6:5f4da9ec47c7

<?xml version="1.0"?>
<tool id="hisat2" name="HISAT" version="2.0.3.1">
    <description>A fast and sensitive alignment program</description>
    <macros>
        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>

        #else if str($input_format.paired.paired_selector) == 'paired_collection':
            -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}"
            @paired_end_options@
        #else:
            -U "${input_format.paired.reads}"
        #end if
        #if $input_format.input_format_selector == 'fasta':
            -f
        #end if
        #if $max_primary:

        #if str($paired_options.paired_options_selector) == "advanced":
            --minins ${paired_options.minins} --maxins ${paired_options.maxins} ${paired_options.no_mixed} ${paired_options.no_discordant}
            ${paired_options.dovetail} ${paired_options.contain} ${paired_options.overlap}
        #end if
        | samtools sort - -@ \${GALAXY_SLOTS:-2} -l 6 -o hsbam > "${output_alignments}"
        ]]>
    </command>
    <inputs>
        <conditional name="input_format">
            <param label="Input data format" name="input_format_selector" type="select">

                  </action>
                </when>
              </conditional>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_format_selector" value="fastq" />
            <param name="paired_selector" value="paired" />

            <param name="reads_r" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />
            <param name="paired_end_options_selector" value="advanced" />
            <param name="no_mixed" value="True" />
            <param name="no_discordant" value="True" />
            <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" />
        </test>
    </tests>
    <help>
        <![CDATA[
Introduction

7:5ba8e317529a

<?xml version="1.0"?>
<tool id="hisat2" name="HISAT2" version="2.0.3.2">
    <description>A fast and sensitive alignment program</description>
    <macros>
        <import>hisat2_macros.xml</import>
    </macros>
    <requirements>

        #else if str($input_format.paired.paired_selector) == 'paired_collection':
            -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}"
            @paired_end_options@
        #else:
            -U "${input_format.paired.reads}"
            #if str( $input_format.paired.unaligned_file ) == "true":
                --un '$output_unaligned_reads_l'
            #end if
            #if str( $input_format.paired.aligned_file ) == "true":
                --al '$output_aligned_reads_l'
            #end if
        #end if
        #if $input_format.input_format_selector == 'fasta':
            -f
        #end if
        #if $max_primary:

        #if str($paired_options.paired_options_selector) == "advanced":
            --minins ${paired_options.minins} --maxins ${paired_options.maxins} ${paired_options.no_mixed} ${paired_options.no_discordant}
            ${paired_options.dovetail} ${paired_options.contain} ${paired_options.overlap}
        #end if
        | samtools sort - -@ \${GALAXY_SLOTS:-2} -l 6 -o hsbam > "${output_alignments}"

        ## Rename any output fastq files
        #if str($input_format.paired.paired_selector) == 'paired' or str($input_format.paired.paired_selector) == 'paired_collection':
            #if $output_unaligned_reads_l and $output_unaligned_reads_r:
                #set left = str($output_unaligned_reads_l).replace(".dat", ".1.dat")
                #set right = str($output_unaligned_reads_l).replace(".dat", ".2.dat")
                && mv '${left}' '${output_unaligned_reads_l}'
                && mv '${right}' '${output_unaligned_reads_r}'
            #end if
            #if $output_aligned_reads_l and $output_aligned_reads_r:
                #set left = str($output_aligned_reads_l).replace(".dat", ".1.dat")
                #set right = str($output_aligned_reads_l).replace(".dat", ".2.dat")
                && mv '${left}' '${output_aligned_reads_l}'
                && mv '${right}' '${output_aligned_reads_r}'
            #end if
        #end if
        ]]>
    </command>
    <inputs>
        <conditional name="input_format">
            <param label="Input data format" name="input_format_selector" type="select">

                  </action>
                </when>
              </conditional>
            </actions>
        </data>
        <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
            <filter>input_format['paired']['unaligned_file'] is True</filter>
            <actions>
                <conditional name="input_format.paired.paired_selector">
                    <when value="single">
                        <action type="format">
                            <option type="from_param" name="input_format.paired.reads" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired">
                        <action type="format">
                            <option type="from_param" name="input_format.paired.reads_f" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired_collection">
                        <action type="format">
                            <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
        <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)" >
            <filter>input_format['paired']['unaligned_file'] is True and input_format['paired']['paired_selector'] != 'single'</filter>
            <actions>
                <conditional name="input_format.paired.paired_selector">
                    <when value="paired">
                        <action type="format">
                            <option type="from_param" name="input_format.paired.reads_r" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired_collection">
                        <action type="format">
                            <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
        <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads${' (L)' if str($input_format.paired.paired_selector) != 'single' else ''}" >
            <filter>input_format['paired']['aligned_file'] is True</filter>
            <actions>
                <conditional name="input_format.paired.paired_selector">
                    <when value="single">
                        <action type="format">
                            <option type="from_param" name="input_format.paired.reads" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired">
                        <action type="format">
                            <option type="from_param" name="input_format.paired.reads_f" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired_collection">
                        <action type="format">
                            <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
        <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)" >
            <filter>input_format['paired']['aligned_file'] is True and input_format['paired']['paired_selector'] != 'single'</filter>
            <actions>
                <conditional name="input_format.paired.paired_selector">
                    <when value="paired">
                        <action type="format">
                            <option type="from_param" name="input_format.paired.reads_r" param_attribute="ext" />
                        </action>
                    </when>
                    <when value="paired_collection">
                        <action type="format">
                            <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_format_selector" value="fastq" />
            <param name="paired_selector" value="paired" />

            <param name="reads_r" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />
            <param name="paired_end_options_selector" value="advanced" />
            <param name="no_mixed" value="True" />
            <param name="no_discordant" value="True" />
            <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" />
        </test>
        <test><!-- testing unaligned output (single dataset) -->
            <param name="input_format_selector" value="fasta" />
            <param name="paired_selector" value="single" />
            <param name="reference_genome_source" value="history" />
            <param name="history_item" value="phiX.fa" ftype="fasta" />
            <param name="unaligned_file" value="true" />
            <param name="aligned_file" value="true" />
            <param name="reference_genome_source" value="history" />
            <param name="history_item" value="phiX.fa" ftype="fasta" />
            <param name="reads" value="test_unaligned_reads.fasta" ftype="fasta" />
            
            <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />
        </test>
        
        <test>
            <param name="input_format_selector" value="fasta" />
            <param name="paired_selector" value="paired" />
            <param name="reference_genome_source" value="history" />
            <param name="history_item" value="phiX.fa" ftype="fasta" />
            <param name="unaligned_file" value="true" />
            <param name="aligned_file" value="true" />
            <param name="reference_genome_source" value="history" />
            <param name="history_item" value="phiX.fa" ftype="fasta" />
            <param name="reads_f" value="test_unaligned_reads.fasta" ftype="fasta" />
            <param name="reads_r" value="test_unaligned_reads.fasta" ftype="fasta" />
            
            <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />
            <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" />
        </test>
    </tests>
    <help>
        <![CDATA[
Introduction