comparison kallisto_pseudo.xml @ 2:1c75aa5de15e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063

1:63f76b9f4ba7

<?xml version="1.0"?>
<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.0">
    <description>- run pseudoalignment on RNA-Seq transcripts</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
        <![CDATA[
        #if $reference_genome.reference_genome_source == "history":
            ln -s '$reference_genome.reference' reference.fa &&
            kallisto index reference.fa -i reference.kallisto &&
            #set index_path = 'reference.kallisto'
        #else:
            #set index_path = $reference_genome.index.fields.path
        #end if
        kallisto pseudo -i '$index_path'
            #if $pseudobam:
                $pseudobam -o .
            #else:

#end if
]]>
        </configfile>
    </configfiles>
    <inputs>
        <conditional name="reference_genome">
            <param name="reference_genome_source" type="select" label="Reference genome for pseudoalignment">
                <option value="indexed" selected="true">Use a built-in genome</option>
                <option value="history">Use a genome from history</option>
            </param>
            <when value="indexed">
                <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy administrator">
                    <options from_data_table="kallisto_indexes">
                        <filter type="sort_by" column="2" />
                        <validator type="no_options" message="No genomes are available for the selected input dataset" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="reference" type="data" format="fasta" label="FASTA reference genome" />
            </when>
        </conditional>
        <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>

            <filter>pseudobam</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="reference_genome_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="umi" value="yes" />
            <param name="forward" ftype="tabular" value="mm10_chrM.umi" />

                <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" />
                <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out1.cells" ftype="tabular" />
            </output>
        </test>
        <test>
            <param name="reference_genome_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="umi" value="no" />
            <param name="reads">

                <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out2.tab" ftype="tabular" />
                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out2.ec" ftype="tabular" />
            </output>
        </test>
        <test>
            <param name="reference_genome_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="sample">
                <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" />
                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" />
            </output>
        </test>
        <test>
            <param name="reference_genome_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="umi" value="no" />
            <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />

                <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out4.tab" ftype="tabular" />
                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out4.ec" ftype="tabular" />
            </output>
        </test>
        <test>
            <param name="reference_genome_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.gz" />

                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" />
            </output>
            <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" />
        </test>
        <test>
            <param name="reference_genome_source" value="cached" />
            <param name="single_paired_selector" value="paired" />
            <param name="collection_selector" value="datasets" />
            <param name="umi" value="yes" />
            <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" />
            <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />

2:1c75aa5de15e

<?xml version="1.0"?>
<tool id="kallisto_pseudo" name="Kallisto pseudo" version="@VERSION@.1">
    <description>- run pseudoalignment on RNA-Seq transcripts</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
        <![CDATA[
        #if $reference_transcriptome.reference_transcriptome_source == "history":
            ln -s '$reference_transcriptome.reference' reference.fa &&
            kallisto index reference.fa -i reference.kallisto &&
            #set index_path = 'reference.kallisto'
        #else:
            #set index_path = $reference_transcriptome.index.fields.path
        #end if
        kallisto pseudo -i '$index_path'
            #if $pseudobam:
                $pseudobam -o .
            #else:

#end if
]]>
        </configfile>
    </configfiles>
    <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>

            <filter>pseudobam</filter>
        </data>
    </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="umi" value="yes" />
            <param name="forward" ftype="tabular" value="mm10_chrM.umi" />

                <discovered_dataset designation="Matrix.ec" file="kallisto_pseudo_out1.ec" ftype="tabular" />
                <discovered_dataset designation="Matrix.cells" file="kallisto_pseudo_out1.cells" ftype="tabular" />
            </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="umi" value="no" />
            <param name="reads">

                <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out2.tab" ftype="tabular" />
                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out2.ec" ftype="tabular" />
            </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="single" />
            <param name="collection_selector" value="collection" />
            <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
            <output name="sample">
                <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out3.tab" ftype="tabular" />
                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out3.ec" ftype="tabular" />
            </output>
        </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="umi" value="no" />
            <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />

                <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out4.tab" ftype="tabular" />
                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out4.ec" ftype="tabular" />
            </output>
        </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.gz" />

                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" />
            </output>
            <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" />
        </test>
        <test>
            <param name="reference_transcriptome_source" value="cached" />
            <param name="single_paired_selector" value="paired" />
            <param name="collection_selector" value="datasets" />
            <param name="umi" value="yes" />
            <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" />
            <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />