comparison featurecounts.xml @ 3:dae123c03a74 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 1c0d28b6cefe154e8cf037c9f36200e8f52a838f

2:a80f96e55958

    <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
    <command><![CDATA[
        ## Check whether all alignments are from the same type (bam || sam)
        featureCounts
            -a "$reference_gene_sets"
            -o "output"
            -T \${GALAXY_SLOTS:-2}

            -t "$extended_parameters.gff_feature_type"
            -g "$extended_parameters.gff_feature_attribute"

                    $extended_parameters.multimapping_enabled.fraction
                #end if

            -Q  $extended_parameters.mapping_quality
                $extended_parameters.largest_overlap
  --minOverlap  $extended_parameters.min_overlap
                $extended_parameters.read_reduction
                $extended_parameters.primary
                $extended_parameters.ignore_dup

                #if str($extended_parameters.read_extension_5p) != "0"

               multiple="false"
               format="bam,sam"
               label="Alignment file"
               help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format" />
        
        <param name="reference_gene_sets"
               format="gff,gtf,gff3"
               type="data"
               label="Gene annotation file"
               help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment" />
        
        <param name="format"
               type="select"
               label="Output format"
               help="The output format will be tabular, select the preferred columns here">

                type="boolean"
                truevalue=" -O"
                falsevalue=""
                argument="-O"
                label="Allow read to contribute to multiple features"
                help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta- feature (or matched feature if -f is specified)" />

            <param name="strand_specificity"
                   type="select"
                   label="Strand specificity of the protocol"
                   argument="-s"

            <param name="read_reduction"
                   type="select"
                   label="Reduce read to single position"
                   argument="--read2pos"
                   help="The read is reduced to its 5' most base or 3'most base. Read summarization is then performed based on thesingle base which the read is reduced to.">
                <option value="" selected="true">Leave the read as it is</option>
                <option value="--read2pos 5">Reduce it to the 5' end</option>
                <option value="--read2pos 3">Reduce it to the 3' end</option>
            </param>
            

                   type="boolean"
                   truevalue=" --primary"
                   falsevalue=""
                   argument="--primary"
                   label="Only count primary alignments"
                   help="If specified, only primary alignments will be counted. Primaryand secondary alignments are identified using bit 0x100 in theFlag field of SAM/BAM files. All primary alignments in a datasetwill be counted no matter they are from multi-mapping reads ornot ('-M' is ignored)." />
            
            <param name="ignore_dup"
                   type="boolean"
                   truevalue=" --ignoreDup"
                   falsevalue=""
                   argument="--ignoreDup"
                   label="Ignore reads marked as duplicate"
                   help="If specified, reads that were marked asduplicates will be ignored. Bit Ox400 in FLAG field of SAM/BAMfile is used for identifying duplicate reads. In paired enddata, the entire read pair will be ignored if at least one endis found to be a duplicate read." />
            
            <param name="count_split_alignments_only"
                   type="boolean"
                   truevalue=" --countSplitAlignmentsOnly"
                   falsevalue=""
                   argument="--countSplitAlignmentsOnly"
                   label="Ignore reads marked as duplicate"
                   help="If specified, only split alignments (CIGARstrings containing letter `N') will be counted. All the otheralignments will be ignored. An example of split alignments isthe exon-spanning reads in RNA-seq data." />
        </section>
    </inputs>
    <outputs>
        <data format="tabular"
              name="output_medium"

        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_short" />
            <param name="include_feature_length_file" value="true"/>
            <output name="output" file="output_1_short.tab"/>
            <output name="output_summary" file="output_1_summary.tab"/>
        </test>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_medium" />
            <param name="include_feature_length_file" value="true"/>
            <output name="output" file="output_1_medium.tab"/>
            <output name="output_summary" file="output_1_summary.tab"/>
        </test>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_full" />
            <param name="include_feature_length_file" value="true"/>
            <output name="output" file="output_1_full.tab"/>
            <output name="output_summary" file="output_1_summary.tab"/>
            <output name="output_feature_lengths" file="output_feature_lengths.tab"/>
        </test>
        
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_short" />
            <param name="include_feature_length_file" value="true"/>
            <output name="output" file="output_2_short.tab"/>
            <output name="output_summary" file="output_2_summary.tab"/>
        </test>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_medium" />
            <param name="include_feature_length_file" value="true"/>
            <output name="output" file="output_2_medium.tab"/>
            <output name="output_summary" file="output_2_summary.tab"/>
        </test>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_full" />
            <param name="include_feature_length_file" value="true"/>
            <output name="output" file="output_2_full.tab"/>
            <output name="output_summary" file="output_2_summary.tab"/>
            <output name="output_feature_lengths" file="output_feature_lengths.tab"/>
        </test>
    </tests>

3:dae123c03a74

    <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
    <command><![CDATA[
        ## Check whether all alignments are from the same type (bam || sam)
        featureCounts
            #if $gtf_source.ref_source=="history":
                -a "$gtf_source.reference_gene_sets"
            #else:
                -a "$gtf_source.reference_gene_sets_builtin.fields.path"
            #end if

            -o "output"
            -T \${GALAXY_SLOTS:-2}

            -t "$extended_parameters.gff_feature_type"
            -g "$extended_parameters.gff_feature_attribute"

                    $extended_parameters.multimapping_enabled.fraction
                #end if

            -Q  $extended_parameters.mapping_quality
                $extended_parameters.largest_overlap
            --minOverlap  $extended_parameters.min_overlap
                $extended_parameters.read_reduction
                $extended_parameters.primary
                $extended_parameters.ignore_dup

                #if str($extended_parameters.read_extension_5p) != "0"

               multiple="false"
               format="bam,sam"
               label="Alignment file"
               help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format" />
        
        <conditional name="gtf_source">
            <param name="ref_source" type="select" label="Gene annotation file">
                <option value="cached">locally cached</option>
                <option value="history">in your history</option>
            </param>
            <when value="cached">
                <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator">
                    <options from_data_table="gene_sets">
                        <filter type="sort_by" column="1" />
                        <validator type="no_options" message="No annotations are available." />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="reference_gene_sets"
                       format="gff,gtf,gff3"
                       type="data"
                       label="Gene annotation file"
                       help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment" />
            </when>
        </conditional>
        
        <param name="format"
               type="select"
               label="Output format"
               help="The output format will be tabular, select the preferred columns here">

                type="boolean"
                truevalue=" -O"
                falsevalue=""
                argument="-O"
                label="Allow read to contribute to multiple features"
                help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta-feature (or matched feature if -f is specified)" />

            <param name="strand_specificity"
                   type="select"
                   label="Strand specificity of the protocol"
                   argument="-s"

            <param name="read_reduction"
                   type="select"
                   label="Reduce read to single position"
                   argument="--read2pos"
                   help="The read is reduced to its 5' most base or 3'most base. Read summarization is then performed based on the single base the the read is reduced to.">
                <option value="" selected="true">Leave the read as it is</option>
                <option value="--read2pos 5">Reduce it to the 5' end</option>
                <option value="--read2pos 3">Reduce it to the 3' end</option>
            </param>
            

                   type="boolean"
                   truevalue=" --primary"
                   falsevalue=""
                   argument="--primary"
                   label="Only count primary alignments"
                   help="If specified, only primary alignments will be counted. Primary and secondary alignments are identified using bit 0x100 in theFlag field of SAM/BAM files. All primary alignments in a dataset will be counted regardless of whether they are from multi-mapping reads or not ('-M' is ignored)." />
            
            <param name="ignore_dup"
                   type="boolean"
                   truevalue=" --ignoreDup"
                   falsevalue=""
                   argument="--ignoreDup"
                   label="Ignore reads marked as duplicate"
                   help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." />
            
            <param name="count_split_alignments_only"
                   type="boolean"
                   truevalue=" --countSplitAlignmentsOnly"
                   falsevalue=""
                   argument="--countSplitAlignmentsOnly"
                   label="Ignore unspliced alignments"
                   help="If specified, only split alignments (CIGAR strings containing the letter `N') will be counted. All the other alignments will be ignored. An example of split alignments are exon-spanning reads in RNA-seq data." />
        </section>
    </inputs>
    <outputs>
        <data format="tabular"
              name="output_medium"

        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_short" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />
            <output name="output" file="output_1_short.tab"/>
            <output name="output_summary" file="output_1_summary.tab"/>
        </test>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_medium" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />
            <output name="output" file="output_1_medium.tab"/>
            <output name="output_summary" file="output_1_summary.tab"/>
        </test>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_full" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />
            <output name="output" file="output_1_full.tab"/>
            <output name="output_summary" file="output_1_summary.tab"/>
            <output name="output_feature_lengths" file="output_feature_lengths.tab"/>
        </test>
        
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_short" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />
            <output name="output" file="output_2_short.tab"/>
            <output name="output_summary" file="output_2_summary.tab"/>
        </test>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_medium" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />
            <output name="output" file="output_2_medium.tab"/>
            <output name="output_summary" file="output_2_summary.tab"/>
        </test>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_full" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />
            <output name="output" file="output_2_full.tab"/>
            <output name="output_summary" file="output_2_summary.tab"/>
            <output name="output_feature_lengths" file="output_feature_lengths.tab"/>
        </test>
    </tests>