comparison chewbbaca_createschema.xml @ 15:1b0a69b7b2c9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 90d84ed39bfd0d34e10cec9f417953042404648a-dirty"

14:1865476fe1e1

<tool id="chewbbaca_createschema" name="chewBBACA CreateSchema" version="2.1.0+galaxy0">
    <description>Create a gene by gene schema based on genomes</description>
    <requirements>
        <requirement type="package" version="2.1.0">chewbbaca</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir assemblies &&
        ln -s
        #for $assembly in $assemblies:

            --ptf '${prodigal_training_file_source.prodigal_training_file}'
          #end if
          #if $cds:
            --CDS '${cds}'
          #end if
          --bsr '${bsr}'
          -o schema
          && tar -czf schema.tgz schema
        ]]>
    </command>
    <inputs>

                </param>
            </when>
            <when value="history">
                <param name="prodigal_training_file" type="data" format="binary"
                       label="Prodigal training file"
                       help=""/>
            </when>
        </conditional>
        <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" />
        <param name="cds" type="data" format="fasta" optional="true" label="Coding sequence file for schema creation (fasta)" />
    </inputs>
    <outputs>
        <data name="schema" type="list" format="fasta" label="${tool.name}: on ${on_string}: Schema">
            <discover_datasets pattern="__name_and_ext__" format="fasta" directory="schema" />
        </data>
        <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz">
        </data>
    </outputs>
    <tests>
        <test>
            <param name="prodigal_training_file_source_selector" value="history" />

15:1b0a69b7b2c9

<tool id="chewbbaca_createschema" name="chewBBACA CreateSchema" version="@TOOL_VERSION@+galaxy0">
    <description>Create a gene by gene schema based on genomes</description>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">chewbbaca</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir assemblies &&
        ln -s
        #for $assembly in $assemblies:

            --ptf '${prodigal_training_file_source.prodigal_training_file}'
          #end if
          #if $cds:
            --CDS '${cds}'
          #end if
          --bsr '${min_bsr}'
          -o schema
          && tar -czf schema.tgz schema
        ]]>
    </command>
    <inputs>

                </param>
            </when>
            <when value="history">
                <param name="prodigal_training_file" type="data" format="binary"
                       label="Prodigal training file"
                       help="Prodigal training file"/>
            </when>
        </conditional>
        <param name="min_bsr" type="float" value="0.6" optional="true" label="Minimum BLAST Score Ratio (BSR) Similarity" />
        <param name="cds" type="data" format="fasta" optional="true" label="Coding sequence file for schema creation (fasta)" />
    </inputs>
    <outputs>
        <data name="schema" type="list" format="fasta" label="${tool.name}: on ${on_string}: Schema">
            <discover_datasets pattern="__name_and_ext__" format="fasta" directory="schema" />
        </data>
        <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz" >
        </data>
    </outputs>
    <tests>
        <test>
            <param name="prodigal_training_file_source_selector" value="history" />