comparison seq_form_db.xml @ 2:3bb9bbecae97 draft default tip

planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty

1:54e716c11b71

<tool id="seq_form_db" name="Get sequences Data From DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Import fragment's data from an accessible DB and export it as .gb files</description>
    <macros>
        <token name="@VERSION_SUFFIX@">2</token>
        <token name="@TOOL_VERSION@">0.3.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="2.2.3">pandas</requirement>
        <requirement type="package" version="2.0.40">sqlalchemy</requirement>
        <requirement type="package" version="2.9.9">psycopg2</requirement>

    </inputs>    
    <outputs>
        <collection name="output_gb" type="list" label="GenBank Files collection" >
            <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" />
        </collection>
        <data name='report' format='txt' label='text report' />
    </outputs>
    <tests>
    <!--manual parameters-->
        <test> 
            <param name="input" value="2-step-golden_gate_plan.csv" />

                    </assert_contents>
                </element>
            </output_collection>
            <output name='report'>
                <assert_contents>
                    <has_n_lines n="1" />
                    <has_line_matching expression="NO missing fragments in DB" />
                </assert_contents>
            </output>
        </test>
        <!--JSON parameters-->
        <test> 

                    </assert_contents>
                </element>
            </output_collection>
            <output name='report'>
                <assert_contents>
                    <has_n_lines n="1" />
                    <has_line_matching expression="NO missing fragments in DB" />
                </assert_contents>
            </output>
        </test>
        <!--test missing fragments-->
        <test> 

                    </assert_contents>
                </element>
            </output_collection>
            <output name='report'>
                <assert_contents>
                    <has_n_lines n="7" />
                    <has_line_matching expression="Missing fragment in DB:" />
                    <has_line_matching expression="ACP10001AaCbbBS" />
                    <has_line_matching expression="NEW20001BbDccKT" />
                    <has_line_matching expression="XYZ10003AaCbbBS" />
                    <has_line_matching expression="CFP10002AaCbbBS" />
                    <has_line_matching expression="ALT30005CcEddLM" />

2:3bb9bbecae97

<tool id="seq_form_db" name="Get sequences Data From DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Import fragment's data from an accessible DB and export it as .gb files</description>
    <macros>
        <token name="@VERSION_SUFFIX@">3</token>
        <token name="@TOOL_VERSION@">0.3.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="2.2.3">pandas</requirement>
        <requirement type="package" version="2.0.40">sqlalchemy</requirement>
        <requirement type="package" version="2.9.9">psycopg2</requirement>

    </inputs>    
    <outputs>
        <collection name="output_gb" type="list" label="GenBank Files collection" >
            <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" />
        </collection>
        <data name='report' format='txt' label='missing fragments' />
    </outputs>
    <tests>
    <!--manual parameters-->
        <test> 
            <param name="input" value="2-step-golden_gate_plan.csv" />

                    </assert_contents>
                </element>
            </output_collection>
            <output name='report'>
                <assert_contents>
                    <has_n_lines n="0" />
                </assert_contents>
            </output>
        </test>
        <!--JSON parameters-->
        <test> 

                    </assert_contents>
                </element>
            </output_collection>
            <output name='report'>
                <assert_contents>
                    <has_n_lines n="0" />
                </assert_contents>
            </output>
        </test>
        <!--test missing fragments-->
        <test> 

                    </assert_contents>
                </element>
            </output_collection>
            <output name='report'>
                <assert_contents>
                    <has_n_lines n="6" />
                    <has_line_matching expression="ACP10001AaCbbBS" />
                    <has_line_matching expression="NEW20001BbDccKT" />
                    <has_line_matching expression="XYZ10003AaCbbBS" />
                    <has_line_matching expression="CFP10002AaCbbBS" />
                    <has_line_matching expression="ALT30005CcEddLM" />