comparison funannotate_compare.xml @ 12:37f9a80ca41e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4

11:0418d28136de

    <requirements>
        <expand macro="requirements" />
    </requirements>
    <version_command>funannotate check --show-versions</version_command>
    <command><![CDATA[
#set $inputs = ""
#for i, f in enumerate($input):
    #set $inputs = $inputs + " input" + str($i) + ".gbk"
    ln -s '$f' input${i}.gbk &&
#end for

#if $run_dnds in ['estimate', 'full']:
    --run_dnds ${run_dnds}
#end if

## need to add --outgroup option some day (hard to get an up to date/customizable list)

--go_fdr ${go_fdr}

--heatmap_stdev ${heatmap_stdev}

        <param name="database" label="Funannotate database" type="select">
            <options from_data_table="funannotate">
                <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="1.0" />
            </options>
        </param>

        <param argument="--run_dnds" type="select" label="Calculate dN/dS ratio on all orthologs">

        </param>

        <param argument="--go_fdr" type="float" value="0.05" label="P-value for FDR GO-enrichment" />
        <param argument="--heatmap_stdev" type="float" value="1.0" label="Cut-off for heatmap" />
        <param argument="--num_orthos" type="integer" value="500" label="Number of Single-copy orthologs to use for ML" />
        <param argument="--proteinortho" type="data" format="tabular" optional="true" label="Proteinortho POFF results" help="TSV format, if available"/>

        <conditional name="ml">
            <param argument="--ml_method" type="select" label="Maximum Likelihood method">
                <option value="iqtree" selected="True">iqtree</option>

        </test>
        <test>
            <param name="input" value="compare/Genus_species.gbk,compare/Other_species.gbk,compare/Other_beast.gbk,compare/Yet_another.gbk" />
            <param name="database" value="2021-07-20-120000" />
            <param name="run_dnds" value="full" />
            <conditional name="ml">
                <param name="ml_method" value="raxml" />
            </conditional>
            <output name="output">
                <assert_contents>

12:37f9a80ca41e

    <requirements>
        <expand macro="requirements" />
    </requirements>
    <version_command>funannotate check --show-versions</version_command>
    <command><![CDATA[
## Needed by some subprocess invoked internally
## https://github.com/nextgenusfs/funannotate/issues/905
export FUNANNOTATE_DB='$database.fields.path' &&

## show detailed info about the reference DB on stdout
funannotate database &&

#set $inputs = ""
#for i, f in enumerate($input):
    #set $inputs = $inputs + " input" + str($i) + ".gbk"
    ln -s '$f' input${i}.gbk &&
#end for

#if $run_dnds in ['estimate', 'full']:
    --run_dnds ${run_dnds}
#end if

#if $outgroup
    --outgroup '$outgroup'
#end if

--go_fdr ${go_fdr}

--heatmap_stdev ${heatmap_stdev}

        <param name="database" label="Funannotate database" type="select">
            <options from_data_table="funannotate">
                <column name="value" index="0" />
                <column name="name" index="1" />
                <column name="path" index="3" />
                <filter type="sort_by" column="0" reverse_sort_order="true"/>
                <filter type="static_value" column="2" value="1.0" />
            </options>
        </param>

        <param argument="--run_dnds" type="select" label="Calculate dN/dS ratio on all orthologs">

        </param>

        <param argument="--go_fdr" type="float" value="0.05" label="P-value for FDR GO-enrichment" />
        <param argument="--heatmap_stdev" type="float" value="1.0" label="Cut-off for heatmap" />
        <param argument="--num_orthos" type="integer" value="500" label="Number of Single-copy orthologs to use for ML" />
        <param argument="--outgroup" type="select" optional="true" label="Outgroup species" help="Name of species to use for ML outgroup. Default: no outgroup">
            <options from_data_table="funannotate_options">
                <column name="value" index="0" />
                <column name="name" index="1" />
                <filter type="static_value" column="2" value="outgroup"/>
                <filter type="param_value" column="3" ref="database"/>
            </options>
        </param>
        <param argument="--proteinortho" type="data" format="tabular" optional="true" label="Proteinortho POFF results" help="TSV format, if available"/>

        <conditional name="ml">
            <param argument="--ml_method" type="select" label="Maximum Likelihood method">
                <option value="iqtree" selected="True">iqtree</option>

        </test>
        <test>
            <param name="input" value="compare/Genus_species.gbk,compare/Other_species.gbk,compare/Other_beast.gbk,compare/Yet_another.gbk" />
            <param name="database" value="2021-07-20-120000" />
            <param name="run_dnds" value="full" />
            <param name="outgroup" value="botrytis_cinerea.dikarya"/>
            <conditional name="ml">
                <param name="ml_method" value="raxml" />
            </conditional>
            <output name="output">
                <assert_contents>