Mercurial > repos > galaxyp > msconvert
annotate msconvert_subset.xml @ 0:ab59b1826345 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
author | galaxyp |
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date | Thu, 22 Oct 2015 14:00:58 -0400 |
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rev | line source |
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0
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
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diff
changeset
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1 <tool id="msconvert_subset" name="msconvert Subset Peak List" version="0.3.0"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
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diff
changeset
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2 <description>against list of scan numbers or indices.</description> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
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3 <!-- |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
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diff
changeset
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4 <requirements> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
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5 <requirement type="package" version="3_0_4388">proteowizard</requirement> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
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changeset
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6 </requirements> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
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7 --> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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8 <command interpreter="python"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
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9 msconvert_wrapper.py |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
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diff
changeset
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10 --input=${input} |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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changeset
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11 --output=${output} |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
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diff
changeset
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12 --fromextension=${input.ext} |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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13 --toextension=${output_type} |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
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diff
changeset
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14 #if $settings.settingsType == "full" |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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15 --binaryencoding=${settings.binary_encoding} |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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16 --mzencoding=${settings.mz_encoding} |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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17 --intensityencoding=${settings.intensity_encoding} |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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18 --zlib=${settings.zlib} |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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19 #end if |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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20 --filter_table="$filter.filterList" |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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21 #if $filter.filterType == "scan_number" |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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22 --filter_table_type="number" |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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23 #else |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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changeset
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24 --filter_table_type="index" |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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25 #end if |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
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changeset
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26 </command> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
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27 |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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changeset
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28 <inputs> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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changeset
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29 <conditional name="type"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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30 <param name="input_type" type="select" label="Input Type"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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31 <option value="mzml">mzML</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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changeset
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32 <option value="mzxml">mzXML</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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changeset
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33 <option value="mgf">mgf</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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34 <option value="ms2">ms2</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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35 </param> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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36 <when value="mzml"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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37 <param format="mzml" name="input" type="data" label="Input mzML"/> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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38 </when> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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39 <when value="mzxml"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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40 <param format="mzxml" name="input" type="data" label="Input mzXML"/> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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41 </when> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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42 <when value="mgf"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
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43 <param format="mgf" name="input" type="data" label="Input mgf"/> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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changeset
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44 </when> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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45 <when value="ms2"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
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46 <param format="ms2" name="input" type="data" label="Input ms2"/> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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47 </when> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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48 </conditional> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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49 <param name="output_type" type="select" label="Output Type"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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50 <option value="mzML">mzML (indexed)</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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51 <option value="unindexed_mzML">mzML (unindexed)</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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52 <option value="mzXML">mzXML (indexed)</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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53 <option value="unindexed_mzXML">mzXML (unindexed)</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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54 <option value="mgf">mgf</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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55 <option value="ms2">ms2</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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56 </param> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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57 <conditional name="filter"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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58 <param name="filterType" type="select" label="Filter by" help=""> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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59 <option value="scan_number" selected="true">Scan Number</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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60 <option value="scan_index">Scan Index</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
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61 </param> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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62 <when value="scan_number"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
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63 <param format="text" name="filterList" type="data" label="Scan Numbers"/> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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changeset
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64 </when> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
changeset
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65 <when value="scan_index"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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66 <param format="text" name="filterList" type="data" label="Scan Indices"/> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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67 </when> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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68 </conditional> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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69 <conditional name="settings"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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70 <param name="settingsType" type="select" label="Advanced msconvert Settings" help=""> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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71 <option value="default">Use Defaults</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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72 <option value="full">Full Parameter List</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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73 </param> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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74 <when value="default" /> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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75 <when value="full"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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76 <param type="select" name="binary_encoding" label="Binary Encoding Precision"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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77 <option value="64" selected="true">64</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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78 <option value="32">32</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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79 </param> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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80 <param type="select" name="mz_encoding" label="m/z Encoding Precision"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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81 <option value="64" selected="true">64</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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82 <option value="32">32</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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83 </param> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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84 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
diff
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85 <option value="64">64</option> |
ab59b1826345
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
galaxyp
parents:
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86 <option value="32" selected="true">32</option> |
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87 </param> |
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88 <param type="boolean" name="zlib" label="Use zlib"> |
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89 </param> |
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90 </when> |
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91 </conditional> |
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92 </inputs> |
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93 <outputs> |
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94 <data format="mzml" name="output" label="${type.input.name.rsplit('.',1)[0]}.${output_type}" > |
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95 <change_format> |
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96 <when input="output_type" value="mzXML" format="mzxml" /> |
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97 <when input="output_type" value="unindexed_mzXML" format="mzxml" /> |
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98 <when input="output_type" value="ms2" format="ms2" /> |
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99 <when input="output_type" value="mgf" format="mgf" /> |
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100 </change_format> |
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101 </data> |
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102 </outputs> |
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103 <help> |
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104 </help> |
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105 </tool> |