annotate dia_umpire_macros.xml @ 0:22a1fa7d9d6a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f

<macros>
    <token name="@VERSION@">2.1.3</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.1.3">dia_umpire</requirement>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
        </stdio>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/nmeth.3255</citation>
            <yield />
        </citations>
    </xml>

    <xml name="common_se_params">
            <param name="SE_Resolution" type="integer" value="" optional="true" label="Resolution" >
                <help>
 SE.Resolution: Used only if the input spectra are stored in profile mode (i.e. not centroided, e.g. by using "Peak Picking" option in MSConvert when converting raw spectral data to mzXML format).
Profile spectra will be centroided using a sliding window. The window is moved across the entire mass range of a spectrum. Only the most intense peak in the window centered at the peak m/z is kept, others are discarded. The window width is calculated based on this parameter as: width = mz / para.Resolution.
Recommended value: Depends on the instrument and acquisition settings. Either check raw data to see the real average resolution of peaks in spectra or consult vendor specifications for the instrument. For AB SCIEX TripleTOF 5600 we use 15000-20000.
                </help>
            </param>

            <param name="SE_StartCharge" type="integer" value="1" min="1" max="10" optional="true" label="StartCharge"> 
                <help>
SE.StartCharge: The minimum charge state for MS1 precursor ion to be detected during isotopic peak grouping.
                </help>
            </param>

            <param name="SE_EndCharge" type="integer" value="5" min="1" max="10" optional="true" label="EndCharge"> 
                <help>
SE.EndCharge: The maximum charge state for MS1 precursor ion to be detected during isotopic peak grouping.
Recommended value: it is not recommended to set this parameter higher than 5 for typical proteomic experiments, as it is unlikely to observe peptides of higher charge states.
                </help>
            </param>

            <param name="SE_MS2StartCharge" type="integer" value="1" min="1" max="10" optional="true" label="MS2StartCharge"> 
                <help>
SE.MS2StartCharge: The minimum charge state for MS2 unfragmented precursor ion to be detected during isotopic peak grouping.
                </help>
            </param>

            <param name="SE_MS2EndCharge" type="integer" value="5" min="1" max="10" optional="true" label="MS2EndCharge"> 
                <help>
SE.MS2EndCharge: The maximum charge state for MS2 unfragmented precursor ion to be detected during isotopic peak grouping.
Recommended value: it is not recommended to set this parameter higher than 5 for typical proteomic experiments, as it is unlikely to observe peptides of higher charge states.
                </help>
            </param>
    </xml>

    <xml name="se_window_params">
            <conditional name="window">
              <param name="WindowType" type="select" label="WindowType">
                <option value="SWATH">SWATH - fixed window size</option>
                <option value="V_SWATH">V_SWATH - variable window size</option>
                <option value="MSX">MSX - 2Da isolation window, its position is shuffled randomly until the whole MS1 range is covered</option>
                <option value="MSE">MSE - as originally implemented in Waters instruments. The full MS1 range is being fragmented at once.</option>
              </param>
              <when value="SWATH">
                <param name="WindowSize" type="integer" value="" optional="true" label="WindowSize"> 
                    <help>
WindowSize: Isolation window size setting for fixed window SWATH. (Please skip this part if the data is from Thermo instrument)
Note: The window size is to be specified including overlapping regions. I.e. if your windows are: 399.5-425.5, 424.5 - 450.5, etc., then the window size should be set to 26.
                    </help>
                </param>
              </when>
              <when value="V_SWATH">
                <!-- should allow a dataset here as well -->
                <conditional name="window_list">
                  <param name="window_list_src" type="select" label="">
                    <option value="history"></option>
                    <option value="text_entry"></option>
                  </param>
                  <when value="history">
                    <param name="WindowListFile" type="data" format="tabular" label="WindowList">
                      <help><![CDATA[
The format should be a tab-delimited list of m/z low and high values, one window per line.  Example:
<pre>
400 451<br>
449 600<br>
</pre>
]]>
                      </help>
                    </param>
                  </when>
                  <when value="text_entry">
                    <param name="WindowList" type="text" area="True" size="40x40" value="" label="WindowList">
                      <help><![CDATA[
The format should be a tab-delimited list of m/z low and high values, one window per line.  Example:
<pre>
400 451<br>
449 600<br>
</pre>
]]>
                      </help>
                    </param>
                  </when>
                </conditional>
              </when>
              <when value="MSX"/>
              <when value="MSE"/>
           </conditional>
    </xml>

</macros>