comparison kallisto_quant.xml @ 10:4f9c4e6566e5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f173f58bc695c22364685c2ffbb9f3e95708f00f

9:2568a3b975cb

                --fragment-length $single_paired.fragment_length
                --sd $single_paired.sd
                '$single_reads'
            #else:
                $single_paired.lib_type
                #if str($single_paired.collection.collection_selector) == 'datasets':
                    #set $forward_reads = $single_paired.collection.forward
                    #set $reverse_reads = $single_paired.collection.reverse
                #else:
                    #set $forward_reads = $single_paired.collection.reads.forward
                    #set $reverse_reads = $single_paired.collection.reads.reverse
                #end if
                #set $reads = "'%s' '%s'" % ($forward_reads, $reverse_reads)
                $reads
            #end if
            $single_overhang

    <inputs>
        <expand macro="reference_input" />
        <conditional name="single_paired">
            <param name="single_paired_selector" type="select" label="Single-end or paired reads">
                <option value="single" selected="true">Single-end</option>
                <option value="paired">Paired</option>
            </param>
            <when value="single">
                <param name="reads" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
                <param argument="--fragment-length" type="integer" value="200" label="Average fragment length" help="Illumina typically produces reads of 180-200bp" />
                <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
            </when>
            <when value="paired">
                <conditional name="collection">
                    <param name="collection_selector" type="select" label="Collection or individual datasets">
                        <option value="datasets" selected="true">Individual files</option>
                        <option value="collection">Pair or list of pairs</option>
                    </param>
                    <when value="datasets">
                        <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />
                        <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />
                    </when>
                    <when value="collection">
                        <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
                    </when>
                </conditional>
                <param name="lib_type" type="select" label="Library strandness information">
                    <option value="">Unstranded</option>
                    <option value="--fr-stranded">Strand specific reads, first read forward</option>
                    <option value="--rf-stranded">Strand specific reads, first read reverse</option>
                </param>
            </when>
        </conditional>
        <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform sequence based bias correction" help="It allows to learn 
            parameters for a model of sequences specific bias and corrects the abundances accordlingly"/>
        <param argument="--bootstrap-samples" type="integer" value="0" label="Number of bootstrap samples" help="Running with bootstraps 

    </outputs>
    <tests>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
            <param name="single_paired_selector" value="paired" />
            <param name="collection_selector" value="datasets" />
            <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
            <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
            <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" />
        </test>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
            <param name="single_paired_selector" value="paired" />
            <param name="collection_selector" value="datasets" />
            <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
            <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
            <param name="lib_type" value="--fr-stranded"/>
            <output name="abundance_tab" >
                <assert_contents>

            </output>
        </test>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
            <param name="single_paired_selector" value="paired" />
            <param name="collection_selector" value="collection" />
            <param name="reads">
                <collection type="paired">
                    <element name="forward" value="mm10_chrM-1.f.fq" />
                    <element name="reverse" value="mm10_chrM-1.r.fq" />
                </collection>

        </test>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
            <param name="single_paired_selector" value="single" />
            <param name="collection_selector" value="collection" />
            <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
            <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />
        </test>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />
            <param name="single_paired_selector" value="paired" />
            <param name="collection_selector" value="datasets" />
            <param name="pseudobam" value="true" />
            <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />
            <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />
            <output name="abundance_tab" file="kallisto_quant_out4.tab" ftype="tabular" />
            <output name="pseudobam_output" file="kallisto_quant_out4.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <param name="reference_transcriptome_source" value="cached" />
            <param name="single_paired_selector" value="paired" />
            <param name="collection_selector" value="datasets" />
            <param name="pseudobam" value="true" />
            <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
            <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />
            <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" />
            <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="hg38_transcripts.fa" />
            <param name="single_paired_selector" value="paired" />
            <param name="collection_selector" value="datasets" />
            <param name="fusion" value="true" />
            <param name="forward" ftype="fastq" dbkey="hg38" value="hg38_F.fq.gz" />
            <param name="reverse" ftype="fastq" dbkey="hg38" value="hg38_R.fq.gz" />
            <output name="fusion_output" file="fusion.txt" ftype="tabular" />
        </test>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="transcripts.fasta" />
            <param name="single_paired_selector" value="paired" />
            <param name="collection_selector" value="datasets" />
            <param name="forward" ftype="fastq" value="reads_forward.fastq.gz" />
            <param name="reverse" ftype="fastq" value="reads_reverse.fastq.gz" />
            <conditional name="genomebam_option">
                <param name="selector" value="--genomebam"/>
                <param name="gtf" value="annotation.gtf.gz"/>

10:4f9c4e6566e5

                --fragment-length $single_paired.fragment_length
                --sd $single_paired.sd
                '$single_reads'
            #else:
                $single_paired.lib_type
                #if str($single_paired.single_paired_selector) == 'paired_single':
                    #set $forward_reads = $single_paired.forward
                    #set $reverse_reads = $single_paired.reverse
                #else:
                    #set $forward_reads = $single_paired.reads.forward
                    #set $reverse_reads = $single_paired.reads.reverse
                #end if
                #set $reads = "'%s' '%s'" % ($forward_reads, $reverse_reads)
                $reads
            #end if
            $single_overhang

    <inputs>
        <expand macro="reference_input" />
        <conditional name="single_paired">
            <param name="single_paired_selector" type="select" label="Single-end or paired reads">
                <option value="single" selected="true">Single-end</option>
                <option value="paired_single">Paired.end (individual files)</option>
                <option value="paired_collection">Paired-end (collections)</option>
            </param>
            <when value="single">
                <param name="reads" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
                <param argument="--fragment-length" type="integer" value="200" label="Average fragment length" help="Illumina typically produces reads of 180-200bp" />
                <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
            </when>
            <when value="paired_single">
                <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />
                <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />
                <expand macro="macro_lib_type"/>
            </when>
            <when value="paired_collection">
                <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
                <expand macro="macro_lib_type"/>
            </when>
        </conditional>
        <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform sequence based bias correction" help="It allows to learn 
            parameters for a model of sequences specific bias and corrects the abundances accordlingly"/>
        <param argument="--bootstrap-samples" type="integer" value="0" label="Number of bootstrap samples" help="Running with bootstraps 

    </outputs>
    <tests>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
            <param name="single_paired_selector" value="paired_single" />
            <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
            <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
            <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" />
        </test>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
            <param name="single_paired_selector" value="paired_single" />
            <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
            <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
            <param name="lib_type" value="--fr-stranded"/>
            <output name="abundance_tab" >
                <assert_contents>

            </output>
        </test>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
            <param name="single_paired_selector" value="paired_collection" />
            <param name="reads">
                <collection type="paired">
                    <element name="forward" value="mm10_chrM-1.f.fq" />
                    <element name="reverse" value="mm10_chrM-1.r.fq" />
                </collection>

        </test>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
            <param name="single_paired_selector" value="single" />
            <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
            <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />
        </test>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />
            <param name="single_paired_selector" value="paired_single" />
            <param name="pseudobam" value="true" />
            <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />
            <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />
            <output name="abundance_tab" file="kallisto_quant_out4.tab" ftype="tabular" />
            <output name="pseudobam_output" file="kallisto_quant_out4.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <param name="reference_transcriptome_source" value="cached" />
            <param name="single_paired_selector" value="paired_single" />
            <param name="pseudobam" value="true" />
            <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
            <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />
            <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" />
            <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" lines_diff="2"/>
        </test>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="hg38_transcripts.fa" />
            <param name="single_paired_selector" value="paired_single" />
            <param name="fusion" value="true" />
            <param name="forward" ftype="fastq" dbkey="hg38" value="hg38_F.fq.gz" />
            <param name="reverse" ftype="fastq" dbkey="hg38" value="hg38_R.fq.gz" />
            <output name="fusion_output" file="fusion.txt" ftype="tabular" />
        </test>
        <test>
            <param name="reference_transcriptome_source" value="history" />
            <param name="reference" ftype="fasta" value="transcripts.fasta" />
            <param name="single_paired_selector" value="paired_single" />
            <param name="forward" ftype="fastq" value="reads_forward.fastq.gz" />
            <param name="reverse" ftype="fastq" value="reads_reverse.fastq.gz" />
            <conditional name="genomebam_option">
                <param name="selector" value="--genomebam"/>
                <param name="gtf" value="annotation.gtf.gz"/>