Mercurial > repos > galaxyp > dia_umpire
annotate macros.xml @ 0:e8f7be6a6e59 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
author | galaxyp |
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date | Tue, 23 Jan 2018 14:45:50 -0500 |
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e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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1 <macros> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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2 <token name="@VERSION@">2.1.3</token> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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3 <xml name="requirements"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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4 <requirements> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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5 <requirement type="package" version="2.1.3">dia_umpire</requirement> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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6 </requirements> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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7 </xml> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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8 <xml name="stdio"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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9 <stdio> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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10 <exit_code range="1:" /> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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11 </stdio> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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12 </xml> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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13 <xml name="citations"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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14 <citations> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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15 <citation type="doi">10.1038/nmeth.3255</citation> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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16 <yield /> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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17 </citations> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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18 </xml> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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19 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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20 <xml name="common_se_params"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
parents:
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21 <param name="SE_Resolution" type="integer" value="" optional="true" label="Resolution" > |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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22 <help> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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23 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). |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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24 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. |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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25 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. |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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26 </help> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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27 </param> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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28 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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29 <param name="SE_StartCharge" type="integer" value="1" min="1" max="10" optional="true" label="StartCharge"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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30 <help> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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31 SE.StartCharge: The minimum charge state for MS1 precursor ion to be detected during isotopic peak grouping. |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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32 </help> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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33 </param> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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34 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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35 <param name="SE_EndCharge" type="integer" value="5" min="1" max="10" optional="true" label="EndCharge"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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36 <help> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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37 SE.EndCharge: The maximum charge state for MS1 precursor ion to be detected during isotopic peak grouping. |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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38 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. |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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39 </help> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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40 </param> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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41 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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42 <param name="SE_MS2StartCharge" type="integer" value="1" min="1" max="10" optional="true" label="MS2StartCharge"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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43 <help> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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44 SE.MS2StartCharge: The minimum charge state for MS2 unfragmented precursor ion to be detected during isotopic peak grouping. |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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45 </help> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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46 </param> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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47 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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48 <param name="SE_MS2EndCharge" type="integer" value="5" min="1" max="10" optional="true" label="MS2EndCharge"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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49 <help> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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50 SE.MS2EndCharge: The maximum charge state for MS2 unfragmented precursor ion to be detected during isotopic peak grouping. |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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51 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. |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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52 </help> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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53 </param> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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54 </xml> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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55 |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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56 <xml name="se_window_params"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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57 <conditional name="window"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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58 <param name="WindowType" type="select" label="WindowType"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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59 <option value="SWATH">SWATH - fixed window size</option> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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60 <option value="V_SWATH">V_SWATH - variable window size</option> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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61 <option value="MSX">MSX - 2Da isolation window, its position is shuffled randomly until the whole MS1 range is covered</option> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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62 <option value="MSE">MSE - as originally implemented in Waters instruments. The full MS1 range is being fragmented at once.</option> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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63 </param> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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64 <when value="SWATH"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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65 <param name="WindowSize" type="integer" value="" optional="true" label="WindowSize"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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66 <help> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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67 WindowSize: Isolation window size setting for fixed window SWATH. (Please skip this part if the data is from Thermo instrument) |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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68 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. |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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69 </help> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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70 </param> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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71 </when> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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72 <when value="V_SWATH"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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73 <!-- should allow a dataset here as well --> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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74 <conditional name="window_list"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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75 <param name="window_list_src" type="select" label=""> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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76 <option value="history"></option> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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77 <option value="text_entry"></option> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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78 </param> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
galaxyp
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79 <when value="history"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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80 <param name="WindowListFile" type="data" format="tabular" label="WindowList"> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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81 <help><![CDATA[ |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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82 The format should be a tab-delimited list of m/z low and high values, one window per line. Example: |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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83 <pre> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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84 400 451<br> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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85 449 600<br> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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86 </pre> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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87 ]]> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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88 </help> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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89 </param> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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90 </when> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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91 <when value="text_entry"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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92 <param name="WindowList" type="text" area="True" size="40x40" value="" label="WindowList"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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93 <help><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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94 The format should be a tab-delimited list of m/z low and high values, one window per line. Example: |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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95 <pre> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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96 400 451<br> |
e8f7be6a6e59
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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97 449 600<br> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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98 </pre> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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99 ]]> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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100 </help> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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101 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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102 </when> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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103 </conditional> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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104 </when> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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105 <when value="MSX"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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106 <when value="MSE"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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107 </conditional> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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108 </xml> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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109 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 5bcb19e47887db334a55235b65eca91c89905fb8
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110 </macros> |