comparison agat.xml @ 6:d6ede73082da draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit df456b8d319fd0a629829fba0f5819117b7936d3

5:e7449b2c14bf

            agat_sp_keep_longest_isoform.pl
                --gff '$input_annotation'
                --config '$agat_configfile'
                --output ./output &&
            cat ./output > '${annotation}'
        #end if
        ]]>
    </command>
        <configfiles>
        <configfile name="agat_configfile"><![CDATA[
#if $tool.selector in ['fix','merge_annotations','complement','splice_sites','filter_feature_fasta','keep_longest_isoform']
---
output_format: $tool.output_format.selector
#if $tool.output_format.selector == "GFF"
gff_output_version: $tool.output_format.version
gtf_output_version: relax

                <option value="fix">Fix and/or standarize GFF3 annotation file (agat_convert_sp_gxf2gxf.pl)</option>
                <option value="functional_analysis">Functional analysis (agat_sp_functional_statistics.pl)</option>
                <option value="merge_annotations">Merge annotations (agat_sp_merge_annotations.pl)</option>
                <option value="functional_annotation">Functional annotation (agat_sp_manage_functional_annotation.pl)</option>
                <option value="keep_longest_isoform">Keep longest isoform (agat_sp_keep_longest_isoform.pl)</option>
            </param>
            <when value="annotation_statistics">
                <expand macro="ANNOTATION_INPUT"/>
                <expand macro="REFERENCE_FASTA"/>
            </when>

            </when>
            <when value="keep_longest_isoform">
                <expand macro="ANNOTATION_INPUT" format="gff,gff3,gff3.gz"/>
                <expand macro="AGAT_CONFIG"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="annotation_gff" format="gff3" label="${tool.name} on ${on_string}: annotation file (GFF)">
            <filter>tool['selector'] == 'convert_GTF2GFF'</filter>
        </data>
        <data name="annotation_gtf" format="gtf" label="${tool.name} on ${on_string}: annotation file (GTF)">
            <filter>tool['selector'] == 'convert_GFF2GTF'</filter>
        </data>
        <data name="annotation" format="gff3" label="${tool.name} on ${on_string}: annotation file">
            <filter>tool['selector'] in ['fix','merge_annotations','complement','filter_feature_fasta','splice_sites','bam2gff','keep_longest_isoform']</filter>
            <change_format>
                <when input="output_format.selector" value="GTF" format="gtf" />
            </change_format>
        </data>
        <data name="sequence_output" format="fasta" label="${tool.name} on ${on_string}: FASTA file">

                <param name="selector" value="keep_longest_isoform"/>
                <param name="gff" value="annotation_dup.gff"/>
            </conditional>
            <output name="annotation" file="test15.gff" ftype="gff3"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

6:d6ede73082da

            agat_sp_keep_longest_isoform.pl
                --gff '$input_annotation'
                --config '$agat_configfile'
                --output ./output &&
            cat ./output > '${annotation}'
        #else if $tool.selector == 'fix_overlapping_genes'
            @input_annotation_single@
            agat_sp_fix_overlaping_genes.pl
                --gff '$input_annotation'
                --config '$agat_configfile'
                --output ./output &&
            cat ./output > '${annotation}'
        #end if
        ]]>
    </command>
        <configfiles>
        <configfile name="agat_configfile"><![CDATA[
#if $tool.selector in ['fix','merge_annotations','complement','splice_sites','filter_feature_fasta','keep_longest_isoform', 'fix_overlapping_genes']
---
output_format: $tool.output_format.selector
#if $tool.output_format.selector == "GFF"
gff_output_version: $tool.output_format.version
gtf_output_version: relax

                <option value="fix">Fix and/or standarize GFF3 annotation file (agat_convert_sp_gxf2gxf.pl)</option>
                <option value="functional_analysis">Functional analysis (agat_sp_functional_statistics.pl)</option>
                <option value="merge_annotations">Merge annotations (agat_sp_merge_annotations.pl)</option>
                <option value="functional_annotation">Functional annotation (agat_sp_manage_functional_annotation.pl)</option>
                <option value="keep_longest_isoform">Keep longest isoform (agat_sp_keep_longest_isoform.pl)</option>
                <option value="fix_overlapping_genes">Fix Overlapping Genes (agat_sp_fix_overlaping_genes.pl)</option>
            </param>
            <when value="annotation_statistics">
                <expand macro="ANNOTATION_INPUT"/>
                <expand macro="REFERENCE_FASTA"/>
            </when>

            </when>
            <when value="keep_longest_isoform">
                <expand macro="ANNOTATION_INPUT" format="gff,gff3,gff3.gz"/>
                <expand macro="AGAT_CONFIG"/>
            </when>
            <when value="fix_overlapping_genes">
                <expand macro="ANNOTATION_INPUT" format="gff,gff3,gff3.gz"/>
                <expand macro="AGAT_CONFIG"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="annotation_gff" format="gff3" label="${tool.name} on ${on_string}: annotation file (GFF)">
            <filter>tool['selector'] == 'convert_GTF2GFF'</filter>
        </data>
        <data name="annotation_gtf" format="gtf" label="${tool.name} on ${on_string}: annotation file (GTF)">
            <filter>tool['selector'] == 'convert_GFF2GTF'</filter>
        </data>
        <data name="annotation" format="gff3" label="${tool.name} on ${on_string}: annotation file">
            <filter>tool['selector'] in ['fix','merge_annotations','complement','filter_feature_fasta','splice_sites','bam2gff','keep_longest_isoform', 'fix_overlapping_genes']</filter>
            <change_format>
                <when input="output_format.selector" value="GTF" format="gtf" />
            </change_format>
        </data>
        <data name="sequence_output" format="fasta" label="${tool.name} on ${on_string}: FASTA file">

                <param name="selector" value="keep_longest_isoform"/>
                <param name="gff" value="annotation_dup.gff"/>
            </conditional>
            <output name="annotation" file="test15.gff" ftype="gff3"/>
        </test>
        <!-- Test 16: Fix overlapping genes -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="fix_overlapping_genes"/>
                <param name="gff" value="test16_input.gff"/>
            </conditional>
            <output name="annotation" file="test16.gff" ftype="gff3"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark