comparison gene_family_classifier.xml @ 3:3e10a2683769 draft

Uploaded

2:8ec75782a05b

<tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="@WRAPPER_VERSION@.2">
    <description>classifies gene sequences into pre-computed orthologous gene family clusters</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements_gene_family_classifier" />
    <command detect_errors="exit_code"><![CDATA[
#if str($options_type.options_type_selector) == 'advanced':
    #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
    #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups
    #set create_orthogroup_cond = $options_type.create_orthogroup_cond

    #end if
#end if

#if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
    --save_hmmscan_log true
    --hmmscan_log '$hmmscan_log'
#end if
#if $create_ortho_sequences:
    #if $create_corresponding_coding_sequences:
        --output_ptorthocs '$output_ptorthocs'
        --output_ptorthocs_dir '$output_ptorthocs.files_path'
    #else:
        --output_ptortho '$output_ptortho'
        --output_ptortho_dir '$output_ptortho.files_path'
    #end if
#end if
#if $single_copy_orthogroup:
    #if $create_ortho_sequences:
        --output_ptsco '$output_ptsco'
        --output_ptsco_dir '$output_ptsco.files_path'
    #end if
#end if
    ]]></command>
    <inputs>
        <param name="input" format="fasta" type="data" label="Proteins fasta file"/>
        <param name="scaffold" type="select" label="Gene family scaffold">

                </conditional>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="hmmscan_log" format="txt" label="${tool.name} (hmmscan.log) on ${on_string}">
            <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
        </data>
        <data name="output_ptortho" format="ptortho" label="${tool.name} (gene family clusters) on ${on_string}">
            <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'no'</filter>
        </data>
        <data name="output_ptorthocs" format="ptorthocs" label="${tool.name} (gene family clusters) on ${on_string}">
            <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'yes'</filter>
        </data>
        <data name="output_ptsco" format="tabular" label="${tool.name} (single copy orthogroups) on ${on_string}">
            <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
            <change_format>
                <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="no" format="ptortho" />
                <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="yes" format="ptorthocs" />
            </change_format>
        </data>
        <collection name="orthos" type="list">
            <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta"/>

            <param name="method" value="orthomcl"/>
            <param name="classifier" value="both"/>
            <param name="options_type_selector" value="advanced"/>
            <param name="create_orthogroup" value="yes"/>
            <param name="create_corresponding_coding_sequences" value="yes"/>
            <output name="output_ptorthocs" file="output.ptorthocs" ftype="ptorthocs"/>
            <output_collection name="orthos" type="list">
                <element name="proteins.blastp.22Gv1.1" file="proteins.blastp.22Gv1.1" ftype="tabular" compare="contains"/>
                <element name="proteins.blastp.22Gv1.1.bestOrthos" file="proteins.blastp.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
                <element name="proteins.both.22Gv1.1.bestOrthos" file="proteins.both.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
                <element name="proteins.both.22Gv1.1.bestOrthos.summary" file="proteins.both.22Gv1.1.bestOrthos.summary" ftype="tabular" compare="contains"/>
                <element name="proteins.hmmscan.22Gv1.1" file="proteins.hmmscan.22Gv1.1" ftype="tabular" compare="contains"/>
                <element name="proteins.hmmscan.22Gv1.1.bestOrthos" file="proteins.hmmscan.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
            </output_collection>
        </test>
    </tests>
    <help>
This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary

3:3e10a2683769

<tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="@WRAPPER_VERSION@.3.0">
    <description>classifies gene sequences into pre-computed orthologous gene family clusters</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.0.3">plant_tribes_gene_family_classifier</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#if str($options_type.options_type_selector) == 'advanced':
    #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
    #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups
    #set create_orthogroup_cond = $options_type.create_orthogroup_cond

    #end if
#end if

#if (str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both') and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
    --save_hmmscan_log true
    --hmmscan_log '$output_hmmscan_log'
#end if
    ]]></command>
    <inputs>
        <param name="input" format="fasta" type="data" label="Proteins fasta file"/>
        <param name="scaffold" type="select" label="Gene family scaffold">

                </conditional>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_hmmscan_log" format="txt" label="${tool.name} (hmmscan.log) on ${on_string}">
            <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
        </data>
        <collection name="output_orthos" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
        </collection>
        <collection name="output_orthogroups_fasta" type="list" label="${tool.name} (gene family clusters) on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_orthogroups_fasta_dir" visible="false" ext="fasta" />
            <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes'</filter>
        </collection>
        <collection name="output_single_copy_fasta" type="list" label="${tool.name} (single copy orthogroups) on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_single_copy_fasta_dir" visible="false" ext="fasta" />
            <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta"/>

            <param name="method" value="orthomcl"/>
            <param name="classifier" value="both"/>
            <param name="options_type_selector" value="advanced"/>
            <param name="create_orthogroup" value="yes"/>
            <param name="create_corresponding_coding_sequences" value="yes"/>
            <param name="coding_sequences" value="transcripts.cleaned.nr.cds" ftype="fasta"/>
            <output_collection name="output_orthos" type="list">
                <element name="proteins.blastp.22Gv1.1" file="proteins.blastp.22Gv1.1" ftype="tabular" compare="contains"/>
                <element name="proteins.blastp.22Gv1.1.bestOrthos" file="proteins.blastp.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
                <element name="proteins.both.22Gv1.1.bestOrthos" file="proteins.both.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
                <element name="proteins.both.22Gv1.1.bestOrthos.summary" file="proteins.both.22Gv1.1.bestOrthos.summary" ftype="tabular" compare="contains"/>
                <element name="proteins.hmmscan.22Gv1.1" file="proteins.hmmscan.22Gv1.1" ftype="tabular" compare="contains"/>
                <element name="proteins.hmmscan.22Gv1.1.bestOrthos" file="proteins.hmmscan.22Gv1.1.bestOrthos" ftype="tabular" compare="contains"/>
            </output_collection>
            <output_collection name="output_orthogroups_fasta" type="list">
                <element name="20.faa" file="20.faa" ftype="fasta"/>
                <element name="20.fna" file="20.fna" ftype="fasta"/>
                <element name="3494.faa" file="3494.faa" ftype="fasta"/>
                <element name="3494.fna" file="3494.fna" ftype="fasta"/>
                <element name="3722.faa" file="3722.faa" ftype="fasta"/>
                <element name="3722.fna" file="3722.fna" ftype="fasta"/>
                <element name="38889.faa" file="38889.faa" ftype="fasta"/>
                <element name="38889.fna" file="38889.fna" ftype="fasta"/>
                <element name="39614.faa" file="39614.faa" ftype="fasta"/>
                <element name="39614.fna" file="39614.fna" ftype="fasta"/>
                <element name="5235.faa" file="5235.faa" ftype="fasta"/>
                <element name="5235.fna" file="5235.fna" ftype="fasta"/>
            </output_collection>
        </test>
    </tests>
    <help>
This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary