comparison agat.xml @ 4:bcc76443a66e draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 28a6a1644ff8ffd8c3a47ccaaad0cb2da2aa87e3

3:7f236c73db6e

            @input_annotation_double@
            agat_sp_compare_two_annotations.pl 
                --gff1 '$input1'
                --gff2 '$input2'
                --output ./temp_output &&
            cat ./temp_output > '${stats_output}'
        #else if $tool.selector == 'extract'
            @input_annotation_single@
            @input_reference@
            agat_sp_extract_sequences.pl
            --gff '$input_annotation'

check_exons: true
check_utrs: true
check_all_level2_locations: true
check_all_level1_locations: true
check_identical_isoforms: true
#end if
        ]]></configfile>
    </configfiles>
    <inputs>
        <conditional name="tool">

                <expand macro="AGAT_CONFIG"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="annotation_gff" format="gff" 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 ${on_string}: annotation file (GTF)">
            <filter>tool['selector'] == 'convert_GFF2GTF'</filter>
        </data>
        <data name="annotation" format="gff" label="${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>

                <conditional name="output_format">
                    <param name="selector" value="gff"/>
                    <param name="version" value="3"/>
                </conditional>
            </conditional>
            <output name="annotation_gff" file="test04.gff" ftype="gff"/>
        </test>
        <!-- Test 05: Convert GFF2GTF -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="convert_GFF2GTF"/>
                <param name="gff" value="test04.gff" ftype="gff"/>
                <param name="gtf_version" value="2"/>
            </conditional>
            <output name="annotation_gtf" file="test05.gtf" ftype="gtf"/>
        </test>
        <!-- Test 06: Convert GTF2GFF -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="convert_GTF2GFF"/>
                <param name="gff" value="annotation_small.gtf" ftype="gtf"/>
            </conditional>
            <output name="annotation_gff" file="test06.gff" ftype="gff"/>
        </test>
        <!-- Test 07: Filter feature FASTA -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="filter_feature_fasta"/>

                <conditional name="reference_genome">
                    <param name="source" value="history"/>
                    <param name="history_item" value="genome.fasta.gz"/>
                </conditional>
            </conditional>
            <output name="annotation" file="test07.gff" ftype="gff"/>
        </test>
        <!-- Test 08: Fix annotation file -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="fix"/>
                <param name="gff" value="annotation_broken.gff" ftype="gff"/>
            </conditional>
            <output name="annotation_gff" file="annotation_fixed.gff" ftype="gff"/>
            <assert_stdout>
                <has_text text="2 exons created that were missing" />
            </assert_stdout>
        </test>
        <!-- Test 09: Functional analysis -->

            </conditional>
            <conditional name="output_format">
                <param name="selector" value="gff"/>
                <param name="version" value="3"/>
            </conditional>
            <output name="annotation_gff" file="test10.gff" ftype="gff"/>
        </test>
        <!-- Test 11: Test compressed files -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="fix"/>
                <param name="gff" value="annotation_broken.gff.gz" ftype="gff"/>
            </conditional>
            <output name="annotation_gff" file="annotation_fixed.gff" ftype="gff"/>
            <assert_stdout>
                <has_text text="2 exons created that were missing" />
            </assert_stdout>
        </test>
        <!-- Test 12:test indexed references -->

        </test>
        <!-- Test 13: Add splicing sites -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="splice_sites"/>
                <param name="gff" value="test04.gff" ftype="gff"/>
            </conditional>
            <output name="annotation" file="test13.gff" ftype="gff"/>
        </test>
        <!-- Test 14: Functional annotation -->
        <test expect_num_outputs="7">
            <conditional name="tool">
                <param name="selector" value="functional_annotation"/>
                <param name="gff" value="annotation_fixed.gff" ftype="gff"/>
                <param name="input_interpro" value="interpro_input.tabular"/>
                <conditional name="blast_adv">
                    <param name="options" value="no"/>
                </conditional>
            </conditional>

        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="keep_longest_isoform"/>
                <param name="gff" value="annotation_dup.gff"/>
            </conditional>
            <output name="annotation" file="test15.gff" ftype="gff"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

4:bcc76443a66e

            @input_annotation_double@
            agat_sp_compare_two_annotations.pl 
                --gff1 '$input1'
                --gff2 '$input2'
                --output ./temp_output &&
            cat ./temp_output/report.txt > '${stats_output}'
        #else if $tool.selector == 'extract'
            @input_annotation_single@
            @input_reference@
            agat_sp_extract_sequences.pl
            --gff '$input_annotation'

check_exons: true
check_utrs: true
check_all_level2_locations: true
check_all_level1_locations: true
check_identical_isoforms: true
clean_attributes_from_template: false
#end if
        ]]></configfile>
    </configfiles>
    <inputs>
        <conditional name="tool">

                <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>

                <conditional name="output_format">
                    <param name="selector" value="gff"/>
                    <param name="version" value="3"/>
                </conditional>
            </conditional>
            <output name="annotation_gff" file="test04.gff" ftype="gff3"/>
        </test>
        <!-- Test 05: Convert GFF2GTF -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="convert_GFF2GTF"/>
                <param name="gff" value="test04.gff" ftype="gff3"/>
                <param name="gtf_version" value="2"/>
            </conditional>
            <output name="annotation_gtf" file="test05.gtf" ftype="gtf"/>
        </test>
        <!-- Test 06: Convert GTF2GFF -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="convert_GTF2GFF"/>
                <param name="gff" value="annotation_small.gtf" ftype="gtf"/>
            </conditional>
            <output name="annotation_gff" file="test06.gff" ftype="gff3"/>
        </test>
        <!-- Test 07: Filter feature FASTA -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="filter_feature_fasta"/>

                <conditional name="reference_genome">
                    <param name="source" value="history"/>
                    <param name="history_item" value="genome.fasta.gz"/>
                </conditional>
            </conditional>
            <output name="annotation" file="test07.gff" ftype="gff3"/>
        </test>
        <!-- Test 08: Fix annotation file -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="fix"/>
                <param name="gff" value="annotation_broken.gff" ftype="gff3"/>
            </conditional>
            <output name="annotation_gff" file="annotation_fixed.gff" ftype="gff3"/>
            <assert_stdout>
                <has_text text="2 exons created that were missing" />
            </assert_stdout>
        </test>
        <!-- Test 09: Functional analysis -->

            </conditional>
            <conditional name="output_format">
                <param name="selector" value="gff"/>
                <param name="version" value="3"/>
            </conditional>
            <output name="annotation_gff" file="test10.gff" ftype="gff3"/>
        </test>
        <!-- Test 11: Test compressed files -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="fix"/>
                <param name="gff" value="annotation_broken.gff.gz" ftype="gff3"/>
            </conditional>
            <output name="annotation_gff" file="annotation_fixed.gff" ftype="gff3"/>
            <assert_stdout>
                <has_text text="2 exons created that were missing" />
            </assert_stdout>
        </test>
        <!-- Test 12:test indexed references -->

        </test>
        <!-- Test 13: Add splicing sites -->
        <test expect_num_outputs="1">
            <conditional name="tool">
                <param name="selector" value="splice_sites"/>
                <param name="gff" value="test04.gff" ftype="gff3"/>
            </conditional>
            <output name="annotation" file="test13.gff" ftype="gff3"/>
        </test>
        <!-- Test 14: Functional annotation -->
        <test expect_num_outputs="7">
            <conditional name="tool">
                <param name="selector" value="functional_annotation"/>
                <param name="gff" value="annotation_fixed.gff" ftype="gff3"/>
                <param name="input_interpro" value="interpro_input.tabular"/>
                <conditional name="blast_adv">
                    <param name="options" value="no"/>
                </conditional>
            </conditional>

        <test expect_num_outputs="1">
            <conditional name="tool">
                <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