comparison das_tool.xml @ 5:b048a987dd7d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit b50985039ff11e1779f9f48f13e3b74fa1c0e955

4:7d997332582e

    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
#set $bins = ""
#set $labels = ""
#set $sep = ""
#for $i, $s in enumerate($binning)
    #set $bins += "%s%s" %($sep, $s.bins)
    #set $labels += "%s%s" %($sep, $s.labels)
    #set $sep = ","
#end for

#if $adv.proteins
    ln -s '$adv.proteins' 'proteins' &&
#end if

DAS_Tool
    --contigs '$contigs'
    --outputbasename 'outputs'
    --bins '$bins'

    ]]></command>
    <inputs>
        <param argument="--contigs" type="data" format="fasta" label="Contig sequences"/>
        <repeat name="binning" title="Bins" min="1">
            <param argument="--bins" type="data" format="tabular" label="Contigs-to-bin table" help="Tabular with two columns: contig-IDs and bin-IDs. Fasta_to_Contigs2Bin can be used to  Converts genome bins in fasta format to Contigs-to-bin table"/>
            <param argument="--labels" type="text" value="" label="Name of binning prediction tool used to generate the table"/>
        </repeat>
        <section name="adv" title="Advanced options">
            <param argument="--search_engine" type="select" label="Engine used for single copy gene identification">
                <option value="diamond" selected="true">diamond</option>
                <option value="blastp">blastp</option>

                    <has_text text="unique_SCGs"/>
                    <has_text text="metabat.8"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <param name="contigs" value="contigs.fasta"/>
            <repeat name="binning">
                <param name="bins" value="metabat.tabular"/>
                <param name="labels" value="metabat"/>

5:b048a987dd7d

    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
#import re

#set $bins = []
#set $labels = []
#for $i, $s in enumerate($binning)
    #silent $bins.append(str($s.bins))
    #if $s.labels != ''
        #silent $labels.append(str($s.labels))
    #else
        #silent $labels.append(re.sub('[^\w\-_\.]', '_', $s.bins.element_identifier))
    #end if
#end for

#if $adv.proteins
    ln -s '$adv.proteins' 'proteins' &&
#end if

#set $bins = ','.join($bins)
#set $labels = ','.join($labels)

DAS_Tool
    --contigs '$contigs'
    --outputbasename 'outputs'
    --bins '$bins'

    ]]></command>
    <inputs>
        <param argument="--contigs" type="data" format="fasta" label="Contig sequences"/>
        <repeat name="binning" title="Bins" min="1">
            <param argument="--bins" type="data" format="tabular" label="Contigs-to-bin table" help="Tabular with two columns: contig-IDs and bin-IDs. Fasta_to_Contigs2Bin can be used to  Converts genome bins in fasta format to Contigs-to-bin table"/>
            <param argument="--labels" type="text" value="" label="Name of binning prediction name" help="If left empty the identifier of the contig-to-bin table is used. Only alphanumeric characters, dash, underscore and dor are allowed. Other characters are replaced by underscore.">
                <sanitizer invalid_char="_">
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="-" />
                        <add value="_" />
                        <add value="." />
                    </valid>
                </sanitizer>
            </param>
        </repeat>
        <section name="adv" title="Advanced options">
            <param argument="--search_engine" type="select" label="Engine used for single copy gene identification">
                <option value="diamond" selected="true">diamond</option>
                <option value="blastp">blastp</option>

                    <has_text text="unique_SCGs"/>
                    <has_text text="metabat.8"/>
                </assert_contents>
            </output>
        </test>
        <!-- like the first test, but with empty label  -->
        <test expect_num_outputs="4">
            <param name="contigs" value="contigs.fasta"/>
            <repeat name="binning">
                <param name="bins" value="metabat.tabular"/>
                <!-- <param name="labels" value="metabat"/> -->
            </repeat>
            <section name="adv">
                <param name="search_engine" value="diamond"/>
                <param name="proteins" value="proteins.fasta"/>
                <param name="score_threshold" value="0.5"/>
                <param name="duplicate_penalty" value="0.6"/>
                <param name="megabin_penalty" value="0.5" />
            </section>
            <section name="output">
                <param name="write_bin_evals" value="true"/>
                <conditional name="write_bins">
                    <param name="write_bins" value=""/>
                </conditional>
                <param name="debug" value="true"/>
            </section>
            <output name="summary" ftype="tabular">
                <assert_contents>
                    <has_text text="unique_SCGs"/>
                    <has_text text="metabat.8"/>
                    <has_text text="bacteria"/>
                </assert_contents>
            </output>
            <output name="contigs2bin" ftype="tabular">
                <assert_contents>
                    <has_text text="Ley3_66761_scaffold_6"/>
                </assert_contents>
            </output>
            <output name="log" ftype="txt">
                <assert_contents>
                    <has_text text="Skipping gene prediction"/>
                    <has_text text="#Target sequences to report alignments for: 1"/>
                </assert_contents>
            </output>
            <output name="eval" ftype="tabular">
                <assert_contents>
                    <has_text text="unique_SCGs"/>
                    <has_text text="metabat.8"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <param name="contigs" value="contigs.fasta"/>
            <repeat name="binning">
                <param name="bins" value="metabat.tabular"/>
                <param name="labels" value="metabat"/>