comparison varvamp.xml @ 1:80e18c0836e5 draft

planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 1626c59de1e3aa8a9ccb8674b38a4654a03ab44b

0:462e62be07e1

    <xrefs>
        <xref type="bio.tools">varvamp</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">varvamp</requirement>
    </requirements>
    <version_command>varvamp --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
VARVAMP_CONFIG=custom_config varvamp

Testing with a new alignment/analysis:

As a first check whether a new alignment of viral sequences can be used with specific settings of the tool, it may help to disable all configurable outputs, which will leave you with only the Analysis Log. This will be enough to see if there are any errors with the combination of alignment and settings, and whether you are on a roughly correct track (varVAMP reports some primers, for example). This way, you're not flooding your analysis history with lots of likely useless datasets, and once you've fixed potential issues you can add back more outputs and rerun the analysis.
    ]]></help>
    <citations>
        <citation type="doi">https://github.com/jonas-fuchs/varVAMP/</citation>
    </citations>
</tool>

1:80e18c0836e5

    <xrefs>
        <xref type="bio.tools">varvamp</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">varvamp</requirement>
        <requirement type="package" version="2.0.1">primer3-py</requirement>
        <requirement type="package" version="0.7.17">seqfold</requirement>
    </requirements>
    <version_command>varvamp --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
VARVAMP_CONFIG=custom_config varvamp

Testing with a new alignment/analysis:

As a first check whether a new alignment of viral sequences can be used with specific settings of the tool, it may help to disable all configurable outputs, which will leave you with only the Analysis Log. This will be enough to see if there are any errors with the combination of alignment and settings, and whether you are on a roughly correct track (varVAMP reports some primers, for example). This way, you're not flooding your analysis history with lots of likely useless datasets, and once you've fixed potential issues you can add back more outputs and rerun the analysis.
    ]]></help>
    <citations>
        <citation type="doi">10.5281/zenodo.10908223</citation>
    </citations>
</tool>