comparison pangolin.xml @ 4:42126b414951 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"

3:514a786baaa9

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">2.3.8</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
        <requirement type="package" version="0.22.0">csvtk</requirement>
    </requirements>

        pangolin
        --threads \${GALAXY_SLOTS:-1}
        #if str($db.source) == "download" or str($db.source) == "builtin"
            --datadir 'datadir'
        #end if
        $alignment
        --outfile report.csv 
        --max-ambig $max_ambig
        --min-length $min_length
        '$input1'

            && mv sequences.aln.fasta '$align1'
        #end if 
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" /> 
        <param name="alignment" type="boolean" label="Generate output alignment" 
            truevalue="--alignment" falsevalue="" /> 
        <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed" 
            value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" />
        <param argument="--min-length" type="integer" label="Minimum query length allowed" 
            value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>

                <param name="db_release" label="pangoLEARN release" type="select">
                    <options from_data_table="pangolearn">
                        <column name="value" index="0" />
                        <column name="name" index="1" />
                        <column name="path" index="3" />
                        <filter type="sort_by" column="0"/>
                    </options>
                </param>
            </when>
            <when value="default">
            </when>
      </conditional>
    </inputs>
    <outputs>
        <data name="output1" format="tabular" label="pangolin on ${on_string}">
            <actions>
                <action name="column_names" type="metadata" default="taxon,lineage,probability,pangoLEARN_version,status,note" />
            </actions>
        </data>
        <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
            <filter>alignment</filter>
        </data>

            <conditional name="db">
                <param name="source" value="download" />
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text text="B.1.1" />
                    <has_text text="passed_qc" />
                    <has_n_lines n="1" />
                </assert_contents>
            </output>
        </test>

            <conditional name="db">
                <param name="source" value="download" />
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text text="B.1.1" />
                    <has_text text="passed_qc" />
                    <has_n_lines n="1" />
                </assert_contents>
            </output>
            <output name="align1" file="aln1.fasta" ftype="fasta">

                    <has_text text="Consensus_EB232-crude-prep_S297" />
                    <has_n_lines n="2" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input1" value="test1.fasta"/>
            <conditional name="db">
                <param name="source" value="builtin" />
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text text="Consensus_EB232-crude-prep_S297" />
                    <has_n_lines n="1" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input1" value="multiple_alignment.fasta.gz"/>
            <conditional name="db">
                <param name="source" value="builtin" />
            </conditional>

                    <has_text text="Poland" />
                    <has_text text="USA" />
                    <has_n_lines n="34" />
                </assert_contents>
            </output>
        </test>
        <!-- test include-header option -->
        <test expect_num_outputs="1">
            <param name="input1" value="multiple_alignment.fasta.gz"/>
            <param name="include_header" value="true" />
            <conditional name="db">
                <param name="source" value="builtin" />
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text text="pangoLEARN_version" />
                    <has_text text="lineage" />

4:42126b414951

<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
    <description>Phylogenetic Assignment of Outbreak Lineages</description>
    <macros>
        <token name="@TOOL_VERSION@">3.0.3</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
        <requirement type="package" version="0.22.0">csvtk</requirement>
    </requirements>

        pangolin
        --threads \${GALAXY_SLOTS:-1}
        #if str($db.source) == "download" or str($db.source) == "builtin"
            --datadir 'datadir'
        #end if
        $usher
        $alignment
        --outfile report.csv 
        --max-ambig $max_ambig
        --min-length $min_length
        '$input1'

            && mv sequences.aln.fasta '$align1'
        #end if 
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" /> 
        <param argument="--usher" type="boolean" label="Use UShER model" truevalue="--usher" falsevalue="" help="Use UShER model instead of default pangoLEARN model" />
        <param argument="--alignment" type="boolean" label="Generate output alignment" 
            truevalue="--alignment" falsevalue="" /> 
        <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed" 
            value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" />
        <param argument="--min-length" type="integer" label="Minimum query length allowed" 
            value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>

                <param name="db_release" label="pangoLEARN release" type="select">
                    <options from_data_table="pangolearn">
                        <column name="value" index="0" />
                        <column name="name" index="1" />
                        <column name="path" index="3" />
                        <filter type="sort_by" column="0" />
                        <filter type="static_value" column="2" value="3.0" />
                    </options>
                </param>
            </when>
            <when value="default">
            </when>
      </conditional>
    </inputs>
    <outputs>
        <data name="output1" format="tabular" label="pangolin on ${on_string}">
            <actions>
                <action name="column_names" type="metadata" default="taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,version,pangolin_version,pangoLEARN_version,pango_version,status,note" />
            </actions>
        </data>
        <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
            <filter>alignment</filter>
        </data>

            <conditional name="db">
                <param name="source" value="download" />
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text_matching expression="B.1.1\t0.0" />
                    <has_text text="passed_qc" />
                    <has_n_lines n="1" />
                </assert_contents>
            </output>
        </test>
        <!-- test UShER mode -->
        <test expect_num_outputs="1">
            <param name="input1" value="test1.fasta"/>
            <param name="usher" value="true" />
            <conditional name="db">
                <param name="source" value="download" />
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text_matching expression="B.1.1.409\t\t*PUSHER" />
                    <has_text text="passed_qc" />
                    <has_n_lines n="1" />
                </assert_contents>
            </output>
        </test>

            <conditional name="db">
                <param name="source" value="download" />
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text_matching expression="B.1.1\t0.0" />
                    <has_text text="passed_qc" />
                    <has_n_lines n="1" />
                </assert_contents>
            </output>
            <output name="align1" file="aln1.fasta" ftype="fasta">

                    <has_text text="Consensus_EB232-crude-prep_S297" />
                    <has_n_lines n="2" />
                </assert_contents>
            </output>
        </test>
        <!-- testing with builtin data is too large -->
        <!-- <test expect_num_outputs="1">
            <param name="input1" value="test1.fasta"/>
            <conditional name="db">
                <param name="source" value="builtin" />
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text text="Consensus_EB232-crude-prep_S297" />
                    <has_n_lines n="1" />
                </assert_contents>
            </output>
        </test> 
        <test expect_num_outputs="1">
            <param name="input1" value="multiple_alignment.fasta.gz"/>
            <conditional name="db">
                <param name="source" value="builtin" />
            </conditional>

                    <has_text text="Poland" />
                    <has_text text="USA" />
                    <has_n_lines n="34" />
                </assert_contents>
            </output>
        </test> -->
        <!-- test include-header option -->
        <test expect_num_outputs="1">
            <param name="input1" value="multiple_alignment.fasta.gz"/>
            <param name="include_header" value="true" />
            <conditional name="db">
                <param name="source" value="download" />
            </conditional>
            <output name="output1" ftype="tabular">
                <assert_contents>
                    <has_text text="pangoLEARN_version" />
                    <has_text text="lineage" />