comparison rna_quast.xml @ 7:3125faf00ffd draft

planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822

6:8e66f695d859

    <command detect_errors="exit_code"><![CDATA[
    mkdir -p './complete_reports/' &&
    mkdir -p './fasta_files/' &&
    #import os, re, glob
    #for $i in $transcripts        
        ln -s '$i' '${re.sub('[^\w\-.]', '_', i.element_identifier)}' &&
    #end for
    #if $reference
        #for $rf in $reference
            ln -s '$rf' '${re.sub('[^\w\-.]', '_', rf.element_identifier)}' &&
        #end for
    #end if
    #if $gene_coordinates.selector == "true"
        #for $g in $gene_coordinates.gtf
            ln -s '$g' '${re.sub('[^\w\-.]', '_', g.element_identifier)}' &&
        #end for
    #end if    
    mkdir outputdir &&
    rnaQUAST.py
    --threads \${GALAXY_SLOTS:-8}
    --transcripts
    #for $i in $transcripts
         '${re.sub('[^\w\-.]', '_', i.element_identifier)}'
    #end for
    #if $reads_option.selector == 'paired'
        --left_reads '${reads_option.forward_reads}'
        --right_reads '${reads_option.reverse_reads}'
    #else if $reads_option.selector == 'single'

        --reads_alignment '${reads_alignment}'
    #end if
    #if $reference
        -r
        #for $rf in $reference
            '${re.sub('[^\w\-.]', '_', rf.element_identifier)}'
        #end for
    #end if
    #if $gene_coordinates.selector == "true"
        --gtf
        #for $g in $gene_coordinates.gtf
            '${re.sub('[^\w\-.]', '_', g.element_identifier)}'
        #end for
        $gene_coordinates.disable_infer_genes
        $gene_coordinates.disable_infer_transcripts
    #end if
    $advanced_options.prokaryote

    #if 'gz' in $output_options.out_add
        && tar -czvf results.tar.gz './outputdir'
    #end if
    
    #if len($transcripts) == 1
        #set $path = "/".join(['outputdir',($transcripts[0].element_identifier).split(".")[0]]) + "_output"
        && mv '${path}' './results'
        ## rename .list files to .txt files to make them detectable
        && find './results/' -name "*.list" -exec mv {} {}.txt \;
        && true
        && printf "************ METRICS/TRANSCRIPTS ***************\n" > stats.txt

        #end if
    #else
        && mkdir -p './results/'
        #if $gene_coordinates.selector == 'true' and $reference
            #for $i, $transcript in enumerate($transcripts)
                #set $path = "/".join(['outputdir',($transcripts[$i].element_identifier).split(".")[0]]) + "_output"
                && rm -r ./results
                && cp -r $path './results'
                && mv ./results/*fasta './fasta_files/'
            #end for
        #end if

                </assert_contents>
            </output>         
        </test>
        <!-- Test 08: Multiple inputs-->
        <test expect_num_outputs="6">
            <param name="transcripts" value="transcriptome01.fasta,transcriptome02.fasta"/>
            <param name="reference" value="reference.fasta"/>
            <conditional name="gene_coordinates">
                <param name="selector" value="true"/>
                <param name="gtf" value="reference.gtf"/>
            </conditional>

            <conditional name="reads_option">
                <param name="selector" value="single"/>
                <param name="single_reads" value="single_end.fastq.gz"/>
            </conditional>
            <output name="short_report_tabular" value="test_08_short_report.tab" ftype="tabular"/>
            <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf"/>
            <output name="stats" value="test_08_complete_report.tab" ftype="txt"  lines_diff="6" />
            <output_collection name="fasta_files" type="list" count="14">
                <element name="transcriptome01.paralogs" file="test_08_paralogs.fasta" ftype="fasta"/>
            </output_collection>
            <output_collection name="list_logs" type="list" count="14">

                        <has_text text="Thank you for using rnaQUAST!"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>

    </tests>
    <help><![CDATA[

.. class:: infomark

7:3125faf00ffd

    <command detect_errors="exit_code"><![CDATA[
    mkdir -p './complete_reports/' &&
    mkdir -p './fasta_files/' &&
    #import os, re, glob
    #for $i in $transcripts        
        ln -s '$i' '${re.sub('[^\w.]', '_', i.element_identifier)}' &&
    #end for
    #if $reference
        #for $rf in $reference
            ln -s '$rf' '${re.sub('[^\w.]', '_', rf.element_identifier)}' &&
        #end for
    #end if
    #if $gene_coordinates.selector == "true"
        #for $g in $gene_coordinates.gtf
            ln -s '$g' '${re.sub('[^\w.]', '_', g.element_identifier)}' &&
        #end for
    #end if    
    mkdir outputdir &&
    rnaQUAST.py
    --threads \${GALAXY_SLOTS:-8}
    --transcripts
    #for $i in $transcripts
         '${re.sub('[^\w.]', '_', i.element_identifier)}'
    #end for
    #if $reads_option.selector == 'paired'
        --left_reads '${reads_option.forward_reads}'
        --right_reads '${reads_option.reverse_reads}'
    #else if $reads_option.selector == 'single'

        --reads_alignment '${reads_alignment}'
    #end if
    #if $reference
        -r
        #for $rf in $reference
            '${re.sub('[^\w.]', '_', rf.element_identifier)}'
        #end for
    #end if
    #if $gene_coordinates.selector == "true"
        --gtf
        #for $g in $gene_coordinates.gtf
            '${re.sub('[^\w.]', '_', g.element_identifier)}'
        #end for
        $gene_coordinates.disable_infer_genes
        $gene_coordinates.disable_infer_transcripts
    #end if
    $advanced_options.prokaryote

    #if 'gz' in $output_options.out_add
        && tar -czvf results.tar.gz './outputdir'
    #end if
    
    #if len($transcripts) == 1
        #set $path = "/".join(['outputdir',re.sub('[^\w.]', '_', $transcripts[0].element_identifier).split(".")[0]]) + "_output"
        && mv '${path}' './results'
        ## rename .list files to .txt files to make them detectable
        && find './results/' -name "*.list" -exec mv {} {}.txt \;
        && true
        && printf "************ METRICS/TRANSCRIPTS ***************\n" > stats.txt

        #end if
    #else
        && mkdir -p './results/'
        #if $gene_coordinates.selector == 'true' and $reference
            #for $i, $transcript in enumerate($transcripts)
                #set $path = "/".join(['outputdir',re.sub('[^\w.]', '_', $transcripts[$i].element_identifier).split(".")[0]]) + "_output"
                && rm -r ./results
                && cp -r $path './results'
                && mv ./results/*fasta './fasta_files/'
            #end for
        #end if

                </assert_contents>
            </output>         
        </test>
        <!-- Test 08: Multiple inputs-->
        <test expect_num_outputs="6">
            <param name="transcripts" value="transcriptome01.fasta,transcriptome?02.fasta"/>
            <param name="reference" value="reference.fasta"/>
            <conditional name="gene_coordinates">
                <param name="selector" value="true"/>
                <param name="gtf" value="reference.gtf"/>
            </conditional>

            <conditional name="reads_option">
                <param name="selector" value="single"/>
                <param name="single_reads" value="single_end.fastq.gz"/>
            </conditional>
            <output name="short_report_tabular" value="test_08_short_report.tab" ftype="tabular"/>
            <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
            <output name="stats" value="test_08_complete_report.tab" ftype="txt"  lines_diff="6" />
            <output_collection name="fasta_files" type="list" count="14">
                <element name="transcriptome01.paralogs" file="test_08_paralogs.fasta" ftype="fasta"/>
            </output_collection>
            <output_collection name="list_logs" type="list" count="14">

                        <has_text text="Thank you for using rnaQUAST!"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <!-- Test 09: Multiple inputs with dash in names-->
        <test expect_num_outputs="6">
            <param name="transcripts" value="transcriptome01.fasta,transcriptome-02.fasta"/>
            <param name="reference" value="reference.fasta"/>
            <conditional name="gene_coordinates">
                <param name="selector" value="true"/>
                <param name="gtf" value="reference.gtf"/>
            </conditional>
            <section name="output_options">
                <param name="out_sr" value="tabular,pdf"/>
            </section>
            <conditional name="use_busco">
                <param name="selector" value="true"/>
                <conditional name="lineage_conditional">
                    <param name="selector" value="cached"/>
                    <param name="cached_db" value="busco-demo-db-20230328"/>
                </conditional>
            </conditional>
            <param name="out_add" value="complete,fasta,logs,gz"/>
            <conditional name="reads_option">
                <param name="selector" value="single"/>
                <param name="single_reads" value="single_end.fastq.gz"/>
            </conditional>
            <output name="short_report_tabular" value="test_08_short_report.tab" ftype="tabular"/>
            <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
            <output name="stats" value="test_08_complete_report.tab" ftype="txt"  lines_diff="6" />
            <output_collection name="fasta_files" type="list" count="14">
                <element name="transcriptome01.paralogs" file="test_08_paralogs.fasta" ftype="fasta"/>
            </output_collection>
            <output_collection name="list_logs" type="list" count="14">
                <element name="STAR.out" ftype="txt">
                    <assert_contents>
                        <has_text text="STAR --runThreadN"/>
                        <has_text text="finished successfully"/>
                    </assert_contents>
                </element>
                <element name="gmap_build.out" ftype="txt">
                    <assert_contents>
                        <has_text text="No alternate scaffolds observed"/>
                    </assert_contents>
                </element>
                <element name="rnaQUAST" ftype="txt">
                    <assert_contents>
                        <has_text text="THE QUALITY OF TRANSCRIPTOME ASSEMBLY DONE"/>
                        <has_text text="Thank you for using rnaQUAST!"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark