comparison gffread.xml @ 5:f312cff50fda draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 35e5b87300fb4e64d6d4eab376012ca9c524a432"

4:0cf496c45054

<tool id="gffread" name="gffread" version="@VERSION@.1">
    <description>Filters and/or converts GFF3/GTF2 records</description>
    <macros>
        <token name="@VERSION@">0.11.4</token>
        <xml name="fasta_output_select">
            <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs">
                <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w exons.fa)</option>
                <option value="-x cds.fa">fasta file with spliced CDS for each GFF transcript (-x cds.fa)</option>
                <option value="-y pep.fa">protein fasta file with the translation of CDS for each record (-y pep.fa)</option>

        <param name="filtering" type="select" display="checkboxes" multiple="true" label="filters">
            <option value="-U">discard single-exon transcripts (-U)</option>
            <option value="-C">coding only: discard mRNAs that have no CDS feature (-C)</option>
            <option value="-G">only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) (-G)</option>
            <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>
            <!-- The no-pseudo option is broken in 0.11.4 of gffread.
                 See https://github.com/gpertea/gffread/issues/43 -->
            <!-- <option value="\-\-no-pseudo">filter out records matching the 'pseudo' keyword (\-\-no-pseudo)</option> -->
        </param>
        <conditional name="region">
            <param name="region_filter" type="select" label="Filter by genome region">
                <option value="none">No</option>
                <option value="filter">Yes</option>

        <test>
            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
            <param name="gff_fmt" value="gff"/>
            <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" />
        </test>

        <test>
            <param name="input" ftype="gtf" value="ecoli-k12.gff3"/>
            <param name="gff_fmt" value="gff"/>
            <param name="full_gff_attribute_preservation" value="-F"/>
            <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" />
        </test>
        
<!-- The no-pseudo option is broken in 0.11.4 of gffread.
     See https://github.com/gpertea/gffread/issues/43 -->
<!-- 
        <test>
            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
            <param name="filtering" value="/-/-no-pseudo"/> # Fix dashes when uncommenting
            <param name="gff_fmt" value="gtf"/>
            <output name="output_gtf">
                <assert_contents>
                    <not_has_text text="pseudo" />
                </assert_contents>
            </output>
        </test>
-->

        <test>
            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
            <param name="region_filter" value="filter"/>
            <param name="range" value="19:496500..504965"/>
            <param name="gff_fmt" value="gtf"/>

                    <has_text text="ENST00000587541" />
                    <has_text text="ENST00000382683" />
                </assert_contents>
            </output>
        </test>

        <test>
            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
            <param name="region_filter" value="filter"/>
            <param name="range" value="19:496500..504965"/>
            <param name="discard_partial" value="true"/>

                    <not_has_text text="ENST00000587541" />
                    <has_text text="ENST00000382683" />
                </assert_contents>
            </output>
        </test>

        <test>
            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
            <param name="filtering" value="-C"/>
            <param name="region_filter" value="filter"/>
            <param name="range" value="19:496500..504965"/>

                    <not_has_text text="ENST00000587541" />
                    <has_text text="ENST00000382683" />
                </assert_contents>
            </output>
        </test>

        <test>
            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
            <param name="source" value="history"/>
            <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/>
            <param name="fa_outputs" value="-w exons.fa,-x cds.fa,-y pep.fa"/>

5:f312cff50fda

<tool id="gffread" name="gffread" version="@VERSION@.0">
    <description>Filters and/or converts GFF3/GTF2 records</description>
    <macros>
        <token name="@VERSION@">0.11.6</token>
        <xml name="fasta_output_select">
            <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs">
                <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w exons.fa)</option>
                <option value="-x cds.fa">fasta file with spliced CDS for each GFF transcript (-x cds.fa)</option>
                <option value="-y pep.fa">protein fasta file with the translation of CDS for each record (-y pep.fa)</option>

        <param name="filtering" type="select" display="checkboxes" multiple="true" label="filters">
            <option value="-U">discard single-exon transcripts (-U)</option>
            <option value="-C">coding only: discard mRNAs that have no CDS feature (-C)</option>
            <option value="-G">only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) (-G)</option>
            <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>
            <option value="--no-pseudo">filter out records matching the 'pseudo' keyword (--no-pseudo)</option>
        </param>
        <conditional name="region">
            <param name="region_filter" type="select" label="Filter by genome region">
                <option value="none">No</option>
                <option value="filter">Yes</option>

        <test>
            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
            <param name="gff_fmt" value="gff"/>
            <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" />
        </test>
        <test>
            <param name="input" ftype="gtf" value="ecoli-k12.gff3"/>
            <param name="gff_fmt" value="gff"/>
            <param name="full_gff_attribute_preservation" value="-F"/>
            <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" />
        </test>
        <test>
            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
            <param name="filtering" value="--no-pseudo"/>
            <param name="gff_fmt" value="gtf"/>
            <output name="output_gtf">
                <assert_contents>
                    <not_has_text text="pseudo" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
            <param name="region_filter" value="filter"/>
            <param name="range" value="19:496500..504965"/>
            <param name="gff_fmt" value="gtf"/>

                    <has_text text="ENST00000587541" />
                    <has_text text="ENST00000382683" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
            <param name="region_filter" value="filter"/>
            <param name="range" value="19:496500..504965"/>
            <param name="discard_partial" value="true"/>

                    <not_has_text text="ENST00000587541" />
                    <has_text text="ENST00000382683" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
            <param name="filtering" value="-C"/>
            <param name="region_filter" value="filter"/>
            <param name="range" value="19:496500..504965"/>

                    <not_has_text text="ENST00000587541" />
                    <has_text text="ENST00000382683" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
            <param name="source" value="history"/>
            <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/>
            <param name="fa_outputs" value="-w exons.fa,-x cds.fa,-y pep.fa"/>