comparison purityX.xml @ 8:b16952cc06d2 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3

7:942e676515fe

        <expand macro="fileload" />

    </inputs>
    <outputs>
	    <data name="purityX_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
              from_work_dir="purityX.tsv" />
        <data name="purityX_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
              from_work_dir="purityX.rdata" />
    </outputs>
    <tests>
        <test>
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes"/>

                <param name="xgroups_value" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15"/>
            </conditional>
            <param name="iw_norm" value="QE5" />
            <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
            <output name="purityX_tsv" value="purityX_output.tsv" />
            <output name="purityX_rdata" value="purityX_output.Rdata" ftype="rdata" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

===================================================================

--------------
Output consists of the mz and intensity of the XCMS features (id based on the XCMS group id) and various
metrics regarding the anticipated precursor ion purity.

============= ============= ============= ================ ================ ================ ================ ================ ================
grpid         mean          median        sd               stde	            RSD              pknm             i                mz
============= ============= ============= ================ ================ ================ ================ ================ ================
1             1.00          1.00          0.0000           0.0000           0.0000           1                5404920          100.0758
------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
2             0.59          0.57          0.3016           0.1508           50.570           3                8793845          101.0084
------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
3             0.08          0.07          0.0784           0.0164           29.643           4                1526502          100.9781
------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
4             1.00          1.00          0.0000           0.0000           0.0000           1                42513139         102.0914
============= ============= ============= ================ ================ ================ ================ ================ ================



    ]]></help>
    <expand macro="citations" />
</tool>

8:b16952cc06d2

        <expand macro="fileload" />

    </inputs>
    <outputs>
	    <data name="purityX_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
              from_work_dir="purityX_output.tsv" />
        <data name="purityX_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
              from_work_dir="purityX_output.RData" />
    </outputs>
    <tests>
        <test>
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes"/>

                <param name="xgroups_value" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15"/>
            </conditional>
            <param name="iw_norm" value="QE5" />
            <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
            <output name="purityX_tsv" value="purityX_output.tsv" />
            <output name="purityX_rdata" value="purityX_output.RData" ftype="rdata" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

===================================================================

--------------
Output consists of the mz and intensity of the XCMS features (id based on the XCMS group id) and various
metrics regarding the anticipated precursor ion purity.

============= ============= ============= ================ ================ ================ ================ ================ ================
grpid         meanPurity    medianPurity  sdPurity         stdePurity	    cvPurity         pknmPurity       i                mz
============= ============= ============= ================ ================ ================ ================ ================ ================
1              1.00          1.00          0.0000           0.0000           0.0000           1                5404920          100.0758
------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
2              0.59          0.57          0.3016           0.1508           50.570           3                8793845          101.0084
------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
3              0.08          0.07          0.0784           0.0164           29.643           4                1526502          100.9781
------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
4              1.00          1.00          0.0000           0.0000           0.0000           1                42513139         102.0914
============= ============= ============= ================ ================ ================ ================ ================ ================


(Note - the additional peakID column is the same as grpid. Included for compatibility with other Galaxy tools)


    ]]></help>
    <expand macro="citations" />
</tool>