comparison glimmer_w_icm.xml @ 3:21d0af260f11 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit a80e3e4aa3a40970af507bf9119cf7f1c2ffb336

2:ce89c473666d

<tool id="glimmer_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@">
    <description>Predict ORFs in prokaryotic genomes (knowlegde-based)</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
    glimmer3
        --max_olap $max_olap
        --gene_len $gene_len

            <when value="free_form">
                <param name="stop_codons" type="text" value="tag,tga,taa" label="Specify stop codons as a comma-separated list" />
            </when>
        </conditional>

        <param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output"/>
        <param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file"/>
    </inputs>
    <outputs>
        <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" />
        <data name="report_output" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)">
            <filter>report == True</filter>
        </data>
        <data name="detailed_output" format="txt" label="Glimmer3 on ${on_string} (detailed report)">
            <filter>detailed_report == True</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="seq_input" value='streptomyces_Tue6071_plasmid_genomic.fasta' />
            <param name="icm_input" value='streptomyces_Tu6071_plasmid_genes.icm' ftype="tar" />
            <param name="max_olap" value="50" />
            <param name="gene_len" value="90" />
            <param name="threshold" value="30" />

            <param name="detailed_report" value="true" />
            <param name="report" value="true" />
            <output name="genes_output" file='glimmer_w_icm_trans-table-11_genomic.fasta' ftype="fasta" />
            <output name="report_output" file='glimmer_w_icm_trans-table-11_genomic.out' ftype="txt" />
            <output name="detailed_output" file='glimmer_w_icm_trans-table-11_genomic.dout' ftype="txt" lines_diff="6" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

3:21d0af260f11

<tool id="glimmer_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
    <description>Predict ORFs in prokaryotic genomes (knowlegde-based)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
    glimmer3
        --max_olap $max_olap
        --gene_len $gene_len

            <when value="free_form">
                <param name="stop_codons" type="text" value="tag,tga,taa" label="Specify stop codons as a comma-separated list" />
            </when>
        </conditional>

        <param name="report" type="boolean" checked="false" label="Report the classic glimmer table output"/>
        <param name="detailed_report" type="boolean" checked="false" label="Output a detailed gene prediction report as separate file"/>
    </inputs>
    <outputs>
        <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" />
        <data name="report_output" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)">
            <filter>report</filter>
        </data>
        <data name="detailed_output" format="txt" label="Glimmer3 on ${on_string} (detailed report)">
            <filter>detailed_report</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="seq_input" value='streptomyces_Tue6071_plasmid_genomic.fasta' />
            <param name="icm_input" value='streptomyces_Tu6071_plasmid_genes.icm' ftype="tar" />
            <param name="max_olap" value="50" />
            <param name="gene_len" value="90" />
            <param name="threshold" value="30" />

            <param name="detailed_report" value="true" />
            <param name="report" value="true" />
            <output name="genes_output" file='glimmer_w_icm_trans-table-11_genomic.fasta' ftype="fasta" />
            <output name="report_output" file='glimmer_w_icm_trans-table-11_genomic.out' ftype="txt" />
            <output name="detailed_output" file='glimmer_w_icm_trans-table-11_genomic.dout' ftype="txt" lines_diff="6" />
        </test>
        <test expect_num_outputs="1">
            <param name="seq_input" value='streptomyces_Tue6071_plasmid_genomic.fasta' />
            <param name="icm_input" value='streptomyces_Tu6071_plasmid_genes.icm' ftype="tar" />
            <param name="max_olap" value="50" />
            <param name="gene_len" value="90" />
            <param name="threshold" value="30" />
            <param name="gc_percent" value="0.0" />
            <param name="linear" value="--linear" />
            <param name="no_indep" value="" />
            <param name="extend" value="" />
            <param name="start_codons" value="atg,gtg,ttg" />
            <param name="genbank_gencode" value="11" />
            <output name="genes_output" file='glimmer_w_icm_trans-table-11_genomic.fasta' ftype="fasta" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**