comparison gene_family_phylogeny_builder.xml @ 5:34ca28db0a5d draft

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4:1134528b93cc

<tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.2">
    <description>builds phylogenetic trees of aligned orthologous gene family clusters</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements_gene_family_phylogeny_builder" />

        #set rooting_order = $rooting_order_file_cond.rooting_order
    #end if
    #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
#end if

python '$__tool_directory__/gene_family_phylogeny_builder.py'
#if str($input_format) == 'ptalign':
    --orthogroup_aln '$input_format_cond.input_ptalign.extra_files_path'
    --alignment_type aln
    --sequence_type protein
#else if str($input_format) == 'ptalignca':

        --rooting_order '$rooting_order'
        ## No else block needed here because the default rooting_order
        ## configuration will be used if the --rooting_order flag is missing.
    #end if
    --bootstrap_replicates $bootstrap_replicates
    --output_phylip '$output_phylip'
    --output_phylip_dir '$output_phylip.files_path'
#end if
--min_orthogroup_size $min_orthogroup_size
--max_orthogroup_size $max_orthogroup_size
--num_threads \${GALAXY_SLOTS:-4}
#if str($output_pttree_dir) == 'yes':
    --output_tree '$output_tree'
    --output_tree_dir '$output_tree.files_path'
#end if
    ]]></command>
    <inputs>
        <conditional name="input_format_cond">
            <param name="input_format" type="select" label="Orthogroup alignments">
                <option value="ptalign">Proteins orthogroup alignments</option>

            </when>
            <when value="fasttree" />
        </conditional>
        <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" />
        <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" />
        <param name="output_pttree_dir" type="select" label="Output additional directory of phylogenetic tree files?">
            <option value="no" selected="true">No</option>
            <option value="yes">Yes</option>
        </param>
    </inputs>
    <outputs>
        <collection name="tree" type="list" label="${tool.name} (phylogenetic trees, dataset collection) on ${on_string}">
            <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
        </collection>
        <data name="output_tree" format="pttree" label="${tool.name} (phylogenetic trees, directory) on ${on_string}">
            <filter>output_pttree_dir == 'yes'</filter>
        </data>
        <data name="output_phylip" format="ptphylip" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}">
            <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
        </data>
    </outputs>
    <tests>
        <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
        <test>
        </test>

5:34ca28db0a5d

<tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.2.1">
    <description>builds phylogenetic trees of aligned orthologous gene family clusters</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements_gene_family_phylogeny_builder" />

        #set rooting_order = $rooting_order_file_cond.rooting_order
    #end if
    #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
#end if

GeneFamilyPhylogenyBuilder
#if str($input_format) == 'ptalign':
    --orthogroup_aln '$input_format_cond.input_ptalign.extra_files_path'
    --alignment_type aln
    --sequence_type protein
#else if str($input_format) == 'ptalignca':

        --rooting_order '$rooting_order'
        ## No else block needed here because the default rooting_order
        ## configuration will be used if the --rooting_order flag is missing.
    #end if
    --bootstrap_replicates $bootstrap_replicates
#end if
--min_orthogroup_size $min_orthogroup_size
--max_orthogroup_size $max_orthogroup_size
--num_threads \${GALAXY_SLOTS:-4}
    ]]></command>
    <inputs>
        <conditional name="input_format_cond">
            <param name="input_format" type="select" label="Orthogroup alignments">
                <option value="ptalign">Proteins orthogroup alignments</option>

            </when>
            <when value="fasttree" />
        </conditional>
        <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" />
        <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" />
    </inputs>
    <outputs>
        <collection name="tree" type="list" label="${tool.name} (phylogenetic trees) on ${on_string}">
            <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
        </collection>
        <collection name="phylip" type="list" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}">
            <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
            <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" format="phylip" />
        </collection>
    </outputs>
    <tests>
        <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
        <test>
        </test>