comparison data_manager/homer_genome_preparse.xml @ 0:e6a2110ac3b9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"

0:e6a2110ac3b9

<tool id="homer_genome_preparse_data_manager" name="Homer genome preparse" tool_type="manage_data" version="@IDX_VERSION@" profile="20.05">
    <requirements>
        <requirement type="package" version="@IDX_VERSION@">homer</requirement>
        <requirement type="package" version="3.9">python</requirement>
    </requirements>
    <macros>
        <token name="@IDX_VERSION@">4.11</token>
    </macros>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/homer_genome_preparse.py'
        '${out_file}'
        --fasta_filename '${all_fasta_source.fields.path}'
        --fasta_dbkey '${all_fasta_source.fields.dbkey}'
        --fasta_description '${all_fasta_source.fields.name}'
        ${mask}
        --size '${size}'
        --index_version '@IDX_VERSION@'
        --data_table_name homer_preparse
    ]]></command>
    <inputs>
        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
            <options from_data_table="all_fasta"/>
        </param>
        <param name="sequence_name" type="text" value="" label="Name of sequence" />
        <param name="sequence_id" type="text" value="" label="ID for sequence" />
        <param name="mask" type="boolean" truevalue="--mask" falsevalue="" checked="False" label="mask repeats/lower case sequence" />
        <param name="size" type="integer" value="200" min="0" label="fragment size to use for motif finding" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="all_fasta_source" value="phiX174"/>
            <output name="out_file" >
                <assert_contents>
                    <has_text text="{&quot;data_tables&quot;: {&quot;homer_preparse&quot;: [{&quot;dbkey&quot;: &quot;phiX174&quot;, &quot;mask&quot;: &quot;False&quot;, &quot;name&quot;: &quot;phiX174 (200bp)&quot;, &quot;path&quot;: &quot;phiX174_200&quot;, &quot;path_fasta&quot;:" />
                    <has_text text="test-data/phiX174.fasta&quot;, &quot;size&quot;: &quot;200&quot;, &quot;value&quot;: &quot;phiX174_200&quot;, &quot;version&quot;: &quot;4.11&quot;}]}}" />
                </assert_contents>                
            </output>
        </test>
        <test>
            <param name="all_fasta_source" value="phiX174"/>
            <param name="mask" value="True"/>
            <param name="size" value="100"/>
            <output name="out_file" >
                <assert_contents>
                    <has_text text="{&quot;data_tables&quot;: {&quot;homer_preparse&quot;: [{&quot;dbkey&quot;: &quot;phiX174&quot;, &quot;mask&quot;: &quot;True&quot;, &quot;name&quot;: &quot;phiX174 masked (100bp)&quot;, &quot;path&quot;: &quot;phiX174r_100&quot;, &quot;path_fasta&quot;:" />
                    <has_text text="test-data/phiX174.fasta&quot;, &quot;size&quot;: &quot;100&quot;, &quot;value&quot;: &quot;phiX174r_100&quot;, &quot;version&quot;: &quot;4.11&quot;}]}}" />
                </assert_contents>                
            </output>
        </test>
    </tests>

    <help>
.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically.
    </help>
</tool>