comparison abims_CAMERA_combinexsAnnos.xml @ 3:4ca5c7bbc6cf draft

planemo upload

2:46e8eb12f47b

<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.1">

    <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description>
    
    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>
        <requirement type="binary">Rscript</requirement>
        <requirement type="package" version="1.44.0">xcms</requirement>
        <requirement type="package" version="1.22.0">camera</requirement>
        <requirement type="package" version="2.1">camera_w4m_script</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>

    <command>
        CAMERA.r 
        xfunction combinexsAnnos image_pos $image_pos image_neg $image_neg
        pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta &amp;&amp; (
        mv variableMetadata.tsv $variableMetadata);
        cat xset.log
    </command>

    <inputs>
        <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />
        <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" />
    

            <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
        </test>
    </tests>
    
    
    <help>

.. class:: infomark

**Authors** Carsten Kuhl [e-mail], Ralf Tautenhahn [e-mail], Steffen Neumann sneumann@@ipb-halle.de

**Example of an xset.combinexsAnnos.variableMetadata.tsv output:**

.. image:: combinexsannos_variableMetadata.png

    </help>

    <citations>
        <citation type="doi"> 10.1021/ac202450g</citation>
        <citation type="doi">10.1093/bioinformatics/btu813</citation>
    </citations>

3:4ca5c7bbc6cf

<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.3">

    <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description>
    
    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>
        <requirement type="binary">Rscript</requirement>
        <requirement type="package" version="1.44.0">xcms</requirement>
        <requirement type="package" version="1.22.0">camera</requirement>
        <requirement type="package" version="2.2.0">camera_w4m_script</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" level="fatal" />
    </stdio>

    <command><![CDATA[
        CAMERA.r 
        xfunction combinexsAnnos 
        image_pos $image_pos 
        image_neg $image_neg

        variableMetadataOutput $variableMetadata

        pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta
        
    ]]></command>

    <inputs>
        <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />
        <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" />
    

            <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
        </test>
    </tests>
    
    
    <help><![CDATA[

.. class:: infomark

**Authors** Carsten Kuhl [e-mail], Ralf Tautenhahn [e-mail], Steffen Neumann sneumann@@ipb-halle.de

**Example of an xset.combinexsAnnos.variableMetadata.tsv output:**

.. image:: combinexsannos_variableMetadata.png


---------------------------------------------------

Changelog/News
--------------

**Version 2.0.3 - 10/02/2016**

- BUGFIX: better management of errors. Datasets remained green although the process failed

- UPDATE: refactoring of internal management of inputs/outputs


**Version 2.0.1 - 07/06/2015**

- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.

- IMPROVEMENT: parameter labels have changed to facilitate their reading.


**Version 2.0.0 - 09/06/2015**

- NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode 


    ]]></help>

    <citations>
        <citation type="doi"> 10.1021/ac202450g</citation>
        <citation type="doi">10.1093/bioinformatics/btu813</citation>
    </citations>