comparison json_db_config_generating_boolean.xml @ 1:34135dac85b0 draft default tip

planemo upload for repository https://github.com/brsynth commit d8cc8b87fdb0374745b5420f2da7f08ae905c222-dirty

0:1a766d8d3883

<tool id="parameters_maystro" name="Parameters Maystro" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Store parameters of tools in a workflow to be used again</description>
    <macros>
        <token name="@VERSION_SUFFIX@">1</token>
        <token name="@TOOL_VERSION@">0.1.0</token>
    </macros>
    <command detect_errors="exit_code"><![CDATA[
        #set $json_files = ' '.join(['"%s"' % file for file in $json_from_workflow])
        #set $json_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $json_from_workflow])
        python '$__tool_directory__/maystro.py'
            --distribute_json '$distribute_json'
            --json_from_workflow $json_files
            --json_from_user '$json_from_user'
            --json_name_mapping $json_name_mapping
            --output_workflow '$output_workflow'
            --output_user '$output_user' && echo 'DEBUB' && cat '$output_user'
    ]]></command>
    <inputs>
        <param name="distribute_json" type="boolean" label="Input Your Parameters As JSON" checked ='false' help="If True user should set workflow parameters as json file" />
        <param name="json_from_workflow" type="data" format="json" multiple="true" optional="true" help='Only if Input Your Parameters As JSON is FALSE' />
        <param name="json_from_user" type="data" format="json" optional="true" help='Only if Input Your Parameters As JSON is TRUE' />
    </inputs>   
    <outputs>
        <data name="output_workflow" format="json" label="workflow param"/>
        <data name="output_user" format="json" label="user_workflow param"/>
    </outputs>
    <tests>
        <!--distribute_json is false-->
        <test> 
            <param name="distribute_json" value='false'/>
            <param name="json_from_workflow" value="seq_from_db_param.json,seq_to_db_param.json"/>
            <output name="output_user">
                <assert_contents>
                    <has_n_lines n="17" />
                </assert_contents>
            </output>
            <output name="output_workflow">
                <assert_contents>
                    <has_n_lines n="0" />
                </assert_contents>
            </output>
        </test>
        <!--distribute_json is true -->
        <test> 
            <param name="distribute_json" value='true'/>
            <param name="json_from_workflow" value="seq_from_db_param.json,seq_to_db_param.json"/>
            <param name="json_from_user" value='merged_test.json'/>
            <output name="output_workflow">
                <assert_contents>
                    <has_n_lines n="17" />
                </assert_contents>
            </output>
            <output name="output_user">
                <assert_contents>
                    <has_n_lines n="0" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Parameters Maystro
===================

Store and Generate a JSON file to be used as a workflow configuration. This JSON file can later be used to pass workflow parameters
This tool is recieve parameters from tools in workflow and return them as a JSON file that can be used later to pass thos parameters again.
    ]]></help>
    <citations>
        <citation type="bibtex">
            @unpublished{json_db_config_generating
                author = {Ramiz Khaled},

1:34135dac85b0

<tool id="parameters_maystro" name="Workflow-0 Parameters Maystro" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Store parameters of workflow-0 to be used again</description>
    <macros>
        <token name="@VERSION_SUFFIX@">3</token>
        <token name="@TOOL_VERSION@">1.1.0</token>
    </macros>
    <command detect_errors="exit_code"><![CDATA[
    #if $user_json and str($user_json) != 'None':
        cp '$user_json' '$output_json'
    #else
        python3 -c "import json; params = {
        'avoid_patterns': '$avoid_patterns',
        'hairpin_constraints': '$hairpin_constraints',
        'gc_constraints': '$gc_constraints',
        'kmer_size': '$kmer_size',
        'execution': '$execution',
        'db_uri': '$db_uri',
        'table': '$table_name',
        'fragment_column': '$fragment_column',
        'sequence_column': '$sequence_column',
        'annotation_column': '$annotation_column'
        }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$output_json'
    #end if
    && echo DEBG && cat '$output_json'
    ]]></command>
    <inputs>
        <param name="avoid_patterns" type="text" area="true" optional="true" label="Avoid Patterns (one per line)" />
        <param name="hairpin_constraints" type="text" area="true" label="Hairpins Constraints" optional="true" help="e.g. (you can add others Hairpins Constraints on a new line): stem_size=20, hairpin_window=200"/>
        <param name="gc_constraints" type="text" area="true" label="Enforce GC Content Constraints" optional="true" help="e.g. (you can add others Enforce GC Content Constraints on a new line): mini=0.3, maxi=0.7, window=100"/>
        <param name="kmer_size" type="integer" label="K-mer Uniqueness Size" value="" optional="true" help="e.g.: 15"/>
        <param name="execution" type="boolean" label="Save To DB ?" checked ='false' optional="true" help="If True data will be saved in the DB" />
        <param name="db_uri" type="text" optional="true" help='Only if Input Your Parameters As JSON is FALSE' />
        <param name="table_name" type="text" optional="true" help='table name in DB' />
        <param name="fragment_column" type="text" optional="true" help='Fragmnet column in DB' />
        <param name="sequence_column" type="text" optional="true" help='Sequence column in DB' />
        <param name="annotation_column" type="text" optional="true" help='Annotation column in DB' />
        <param name="user_json" type="data" format="json" optional="true" help='Only if Input Your Parameters As JSON is TRUE' />
    </inputs>   
    <outputs>
        <data name="output_json" format="json" label="Workflow-0 Parameters"/>
    </outputs>
    <tests>
        <!--manual parameters set-->
        <test> 
            <param name="avoid_patterns" value="BsaI_site
            BsmBI_site
            BbsI_site
            SapI_site
            8x1mer
            5x3mer
            9x2mer" />
            <param name="hairpin_constraints" value='stem_size=20, hairpin_window=200'/>
            <param name="gc_constraints" value="mini=0.3, maxi=0.7, window=100
            mini=0.1, maxi=0.9, window=100"/>
            <param name="kmer_size" value="15" />
            <param name="execution" value="true" />
            <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
            <param name="table_name" value="sample" />
            <param name="fragment_column" value="fragment" />
            <param name="sequence_column" value="sequence" />
            <param name="annotation_column" value="annotation" />
            <output name="output_json">
                <assert_contents>
                    <has_n_lines n="12" />
                </assert_contents>
            </output>
        </test>
        <!--JSON parameters set-->
        <test> 
            <param name="user_json" value='test_json.json'/>
            <output name="output_json">
                <assert_contents>
                    <has_n_lines n="12" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Parameters Maystro
===================

Store and Generate a JSON file to be used as workflow-0 configuration. This JSON file can later be used as input to pass workflow-0 parameters

    ]]></help>
    <citations>
        <citation type="bibtex">
            @unpublished{json_db_config_generating
                author = {Ramiz Khaled},