comparison dram_strainer.xml @ 3:f081f73cc0be draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 3234c3d93fa294fa9c2c5148eae4b399d42904d8

2:9c8f2cfb70ba

    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
DRAM.py strainer
--input_annotations '$input_annotations'
--input_fasta '$input_fasta'
--output_fasta '$output_fasta'
#if $advanced.fastas:
    --fastas '$advanced.fastas'
#end if

    --genes '$advanced.genes'
#end if
#if $advanced.identifiers:
    --identifiers '$advanced.identifiers'
#end if
## Broken in 3.5.1 - https://github.com/WrightonLabCSU/DRAM/issues/194
##if $advanced.categories:
##    --categories '$advanced.categories'
##end if
#if $advanced.custom_distillate:
    --custom_distillate '$advanced.custom_distillate'
#end if
    ]]></command>
    <inputs>
        <param argument="--input_annotations" type="data" format="tabular" label="Annotations file" help="Produced by the DRAM annotate tool"/>
        <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file to filter"/>
        <section name="advanced" title="Advanced options" expanded="false">
            <param argument="--fastas" type="text" value="" label="Space-separated list of fastas to keep" help="Optional, leave blank to ignore">
                <expand macro="sanitizer"/>
            </param>

                <expand macro="sanitizer"/>
            </param>
            <expand macro="genes_param"/>
            <expand macro="identifiers_param"/>
            <expand macro="custom_distillate_param"/>
            <!-- Broken in 3.5.1, see above -->
            <!-- <expand macro="categories_param"/> -->
        </section>
    </inputs>
    <outputs>
        <data name="output_fasta" format="fasta"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_annotations" ftype="tabular" value="annotated1.tabular"/>
            <param name="input_fasta" ftype="fasta.gz" value="strainer_input_fasta1.fasta.gz"/>
            <param name="fastas" value="dataset_"/>
            <param name="scaffolds" value="scaffold_"/>
            <param name="identifiers" value="K15023"/>
            <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/>
            <output name="output_fasta" ftype="fasta" value="strainer_output1.fasta"/>
       </test>
    </tests>
    <help>
**What it does**

3:f081f73cc0be

    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
DRAM.py strainer
--input_tsv '$input_tsv'
--input_fasta '$input_fasta'
--output_fasta '$output_fasta'
#if $advanced.fastas:
    --fastas '$advanced.fastas'
#end if

    --genes '$advanced.genes'
#end if
#if $advanced.identifiers:
    --identifiers '$advanced.identifiers'
#end if
#if $advanced.categories:
    --categories '$advanced.categories'
#end if
#if $advanced.custom_distillate:
    --custom_distillate '$advanced.custom_distillate'
#end if
    ]]></command>
    <inputs>
        <param argument="--input_tsv" type="data" format="tabular" label="Annotations file" help="Produced by the DRAM annotate tool"/>
        <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file to filter"/>
        <section name="advanced" title="Advanced options" expanded="false">
            <param argument="--fastas" type="text" value="" label="Space-separated list of fastas to keep" help="Optional, leave blank to ignore">
                <expand macro="sanitizer"/>
            </param>

                <expand macro="sanitizer"/>
            </param>
            <expand macro="genes_param"/>
            <expand macro="identifiers_param"/>
            <expand macro="custom_distillate_param"/>
            <expand macro="categories_param"/>
        </section>
    </inputs>
    <outputs>
        <data name="output_fasta" format="fasta"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_tsv" value="annotated1.tabular" ftype="tabular"/>
            <param name="input_fasta" value="strainer_input_fasta1.fasta.gz" ftype="fasta.gz"/>
            <param name="fastas" value="dataset_"/>
            <param name="scaffolds" value="scaffold_"/>
            <param name="identifiers" value="K15023"/>
            <param name="custom_distillate" value="distill_custom.tabular" ftype="tabular"/>
            <output name="output_fasta" ftype="fasta" value="strainer_output1.fasta"/>
       </test>
    </tests>
    <help>
**What it does**