annotate dram_strainer.xml @ 2:9c8f2cfb70ba draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit a5e28ac40a63a269100ddec5629aee5256ce00ef

<tool id="dram_strainer" name="DRAM strain annotations" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>down to genes of interest</description>
    <macros>
        <import>macros.xml</import>
    </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
#if $advanced.scaffolds:
    --scaffolds '$advanced.scaffolds'
#end if
#if $advanced.genes:
    --genes '$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>
            <param argument="--scaffolds" type="text" value="" label="Space-separated list of scaffolds to keep" help="Optional, leave blank to ignore">
                <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**
 
@WHATITDOESHEADER@

This tool accepts a tabular file with all gene annotations from Pfam, UniProt, dbCAN and MEROPS databases produced by the
DRAM annotate tool and strains them, further analyzing genes of interest by making trees of functional models.

@CUSTOMDISTILLATEFILES@

**Options**

 * **Space-separated list of fastas to keep** - space-separated list of fastas to keep
 * **Space-separated list of scaffolds to keep** - space-separated list of scaffolds to keep
 * **Space-separated list of genes to keep** - space-separated list of genes to keep
 * **Database identifiers** - database identifiers to keep

@WHATITDOESFOOTER@
    </help>
    <expand macro="citations"/>
</tool>