comparison chimera.vsearch.xml @ 7:de3cfb122105 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"

6:12e856482d26

<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.1">
    <description>find potential chimeric sequences using vsearch</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

    <outputs>
        <expand macro="logfile-output"/>
        <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: vsearch.chimeras"/>
        <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: vsearch.accnos"/>
        <data name="out_count" format="mothur.count_table" from_work_dir="template.*vsearch.pick.count_table" label="${tool.name} on ${on_string}: vsearch.count_table">
            <filter>template['source'] == 'self' and template['count']</filter>
        </data>
    </outputs>
    <tests>
        <test><!-- de novo test with name file -->
            <param name="fasta" value="stool_small.unique.fasta"/>
            <param name="source" value="names"/>
            <param name="name" value="stool_small.names"/>
            <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/>
            <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- de novo test with count table-->
            <param name="fasta" value="chimera.fasta"/>
            <param name="source" value="self"/>
            <param name="count" value="chimera.count_table"/>
            <param name="dereplicate" value="true"/>
            <output name="vsearch.chimeras" file="chimera.vsearch.chimeras" ftype="txt"/>
            <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos"/>
            <output name="out_count" file="chimera.vsearch.count_table" ftype="mothur.count_table"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with reference file -->
            <param name="fasta" value="stool_small.unique.fasta"/>
            <param name="source" value="hist"/>
            <param name="reference" value="stool_small.unique.fasta"/>
            <output name="vsearch.chimeras" ftype="txt">
                <assert_contents>

7:de3cfb122105

<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.2">
    <description>find potential chimeric sequences using vsearch</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

    <outputs>
        <expand macro="logfile-output"/>
        <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: vsearch.chimeras"/>
        <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: vsearch.accnos"/>
        <data name="out_count" format="mothur.count_table" from_work_dir="template.*vsearch.pick.count_table" label="${tool.name} on ${on_string}: vsearch.count_table">
            <filter>template['source'] == 'self' and template['count'] and template['count'].metadata.groups != []</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="3"><!-- de novo test with name file -->
            <param name="fasta" value="stool_small.unique.fasta"/>
            <param name="source" value="names"/>
            <param name="name" value="stool_small.names"/>
            <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/>
            <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test expect_num_outputs="4"><!-- de novo test with count table-->
            <param name="fasta" value="chimera.fasta"/>
            <param name="source" value="self"/>
            <param name="count" value="chimera.count_table" ftype="mothur.count_table"/>
            <param name="dereplicate" value="true"/>
            <output name="vsearch.chimeras" file="chimera.vsearch.chimeras" ftype="txt"/>
            <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos" sort="true"/>
            <output name="out_count" file="chimera.vsearch.count_table" ftype="mothur.count_table"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test expect_num_outputs="3"><!-- de novo test with count table (missing group info)-->
            <param name="fasta" value="chimera.fasta"/>
            <param name="source" value="self"/>
            <param name="count" value="chimera.count_table_wogroups" ftype="mothur.count_table"/>
            <param name="dereplicate" value="true"/>
            <!-- for some reason only for count tables wo group info header is printed -->
            <output name="vsearch.chimeras" file="chimera.vsearch.chimeras_wogroups" ftype="txt"/>
            <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos" sort="true"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test expect_num_outputs="3"><!-- test with reference file -->
            <param name="fasta" value="stool_small.unique.fasta"/>
            <param name="source" value="hist"/>
            <param name="reference" value="stool_small.unique.fasta"/>
            <output name="vsearch.chimeras" ftype="txt">
                <assert_contents>