Mercurial > repos > rjmw > dimspy_process_scans

annotate process_scans.xml @ 1:769165c75514 draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
author rjmw
date Wed, 30 May 2018 09:20:20 -0400
parents d129e75a31d9
children
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d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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1 <tool id="dimspy_process_scans" name="Process Scans (and SIM-Stitch)" version="1.0.0">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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2 <description> - Read, filter and average MS scans</description>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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3 <macros>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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4 <import>macros.xml</import>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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5 </macros>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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6 <expand macro="requirements" />
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769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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7 <command detect_errors="exit_code">
769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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8 <![CDATA[
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d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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9 #if $input.format == "data_collection"
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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10 #for $fn in $input.source
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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11 #if str( $fn ).endswith(".dat")
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769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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12 ln -s '$fn' '$fn.name'
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d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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13 &&
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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14 #end if
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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15 #end for
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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16 #elif $input.format == "single_file"
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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17 #if str( $input.source ).endswith(".dat")
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769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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18 ln -s '$input.source' '$input.source.name'
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d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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19 &&
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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20 #end if
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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21 #end if
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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22 dimspy process-scans
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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23 #if $input.format == "data_collection"
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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24 #for $fn in $input.source
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769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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25 --input '$fn.name'
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d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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26 #end for
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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27 #elif $input.format == "single_file"
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769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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28 --input '$input.source.name'
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d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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29 #elif $input.format == "library"
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769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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30 --input '$__app__.config.user_library_import_dir/$__user_email__/$input.source'
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d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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31 #else
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769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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32 --input '$input.source'
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d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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33 #end if
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769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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34 --output '$hdf5_file_out'
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d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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35 #if $filelist
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769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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36 --filelist '$filelist'
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d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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37 #end if
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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38 --function-noise $function_noise
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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39 --snr-threshold $snr_threshold
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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40 --ppm $mults.ppm
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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41 --min_scans $mults.min_scans
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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42 #if float($mults.min_fraction) > 0.0
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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43 --min-fraction $mults.min_fraction
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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44 #else
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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45 --min-fraction 0.0
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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46 #end if
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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47 #if float($mults.rsd_threshold) > 0.0
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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48 --rsd-threshold $mults.rsd_threshold
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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49 #end if
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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50 #if $adv.skip_stitching
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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51 --skip-stitching
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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52 #end if
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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53 #if float($adv.ringing_threshold) > 0.0
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769165c75514 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
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54 --ringing-threshold $adv.ringing_threshold
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d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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55 #end if
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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56 #for $mzr in $adv.remove_mz_range
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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57 --remove-mz-range $mzr.start $mzr.end
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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58 #end for
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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59 #if $scan_events.filter == "true"
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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60 #for $se in $scan_events.descriptions
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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61 #if $scan_events.incl_excl == "include"
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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62 --include-scan-events $se.start $se.end $se.scan_type
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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63 #elif $scan_events.incl_excl == "exclude"
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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64 --exclude-scan-events $se.start $se.end $se.scan_type
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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65 #end if
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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66 #end for
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67 #end if
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68 --report '$report'
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69 &&
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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70 dimspy hdf5-pls-to-txt
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71 --input '$hdf5_file_out'
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72 --output .
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73 --delimiter $delimiter
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74 ]]>
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75 </command>
0
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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76 <inputs>
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77 <conditional name="input">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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78 <param name="format" type="select" label="Choose the source for the dataset" >
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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79 <option value="zip_file" selected="true">Zip file from your History containing *.mzML files</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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80 <option value="library">Library directory name</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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81 <option value="data_collection">Data collection (*.mzML or *.raw files)</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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82 <option value="single_file">Single *.mzML or *.raw file</option>
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83 </param>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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84 <when value="zip_file">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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85 <param name="source" type="data" format="zip" label="Zip file containing *.mzml or *.raw files" argument="--source">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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86 <validator type="empty_field" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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87 </param>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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88 </when>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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89 <when value="library">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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90 <param name="source" type="text" size="40" label="Library directory containing *.mzml or *.raw files" argument="--source">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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91 <validator type="empty_field" />
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92 </param>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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93 </when>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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94 <when value="data_collection">
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95 <param name="source" type="data_collection" format="mzml,thermo.raw,raw" label="Data collection of *.mzml or *.raw files" argument="--source" >
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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96 <validator type="empty_field" />
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97 </param>
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98 </when>
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99 <when value="single_file">
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100 <param name="source" type="data" format="mzml,thermo.raw,raw" label="Single *.mzml or *.raw" argument="--source" >
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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101 <validator type="empty_field" />
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102 </param>
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103 </when>
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104 </conditional>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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105 <param name="filelist" type="data" optional="true" format="tsv,tabular" label="Filelist / Samplelist" argument="--filelist" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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106 <param name="function_noise" type="select" label="Function to calculate the noise from each scan" help="" argument="--function-noise">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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107 <option value="median" selected="true">median intensity</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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108 <option value="mean">mean intensity</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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109 <option value="mad">mad (mean absolute deviation) intensity</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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110 <option value="noise_packets">As shown in Xcalibur Qual Browser (Available for *.RAW files only)</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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111 </param>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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112 <param name="snr_threshold" type="float" value="3.0" label="Signal-to-noise ratio threshold" help="" argument="--snr-threshold" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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113 <conditional name="scan_events">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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114 <param name="filter" type="boolean" label="Filter specific windows or scan events?" help="(--include-scan-events / --exclude-scan-events)"/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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115 <when value="true">
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116 <param name="incl_excl" type="select" label="Include / Exclude scan event(s)" >
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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117 <option value="exclude" selected="true">Exclude</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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118 <option value="include">Include</option>
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119 </param>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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120 <repeat name="descriptions" title="Description">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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121 <param name="start" type="float" value="0" label="Start m/z for scan event"/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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122 <param name="end" type="float" value="0" label="End m/z for scan event">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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123 <validator type="expression" message="M/z value must be larger than 0.0">float(value) > 0.0</validator>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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124 </param>
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125 <param name="scan_type" type="select" label="Scan type">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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126 <option value="full" selected="true">Full scan</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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127 <option value="sim">SIM scan</option>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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128 </param>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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129 </repeat>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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130 </when>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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131 <when value="false">
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132 </when>
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133 </conditional>
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134 <section name="mults" title="Show options for multiple scans" expanded="True">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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135 <param name="min_scans" type="integer" value="1" min="1" label="Minimum number of scans required for each m/z window or event" help="" argument="--min_scans" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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136 <param name="ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation in consecutive scans in parts per million." argument="--ppm" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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137 <param name="min_fraction" min="0.0" max="1.0" type="float" value="0.0" label="Minimum fraction (i.e. percentage) of scans a peak has to be present in." help="Select '0' to skip this step." argument="--min-fraction" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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138 <param name="rsd_threshold" type="float" value="0.0" min="0.0" label="Relative standard deviation threshold" help="Select '0' to skip this step. Maximum tolerated relative standard deviation (RSD) of the peak intensities across scans." argument="--rsd-threshold" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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139 </section>
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140 <section name="adv" title="Show advanced options" expanded="True">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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141 <param name="skip_stitching" type="boolean" value="false" label="Skip SIM-Stitching?" help="When set to 'yes' it will skip the processing step where (SIM) windows are 'stitched' or 'joined' together. Set this option to 'yes' if you like to proces individual scan/SIM windows (events/ranges) without 'stitching' them."/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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142 <repeat name="remove_mz_range" title="Remove m/z range(s)?">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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143 <param name="start" type="float" value="0.0" label="Start m/z of removal range"/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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144 <param name="end" type="float" value="0.0" label="End m/z of removal range">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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145 <validator type="expression" message="M/z value must be larger than 0.0">float(value) > 0.0</validator>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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146 </param>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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147 </repeat>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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148 <param name="ringing_threshold" type="float" value="0.0" min="0.0" max="1.0" label="Relative intensity threshold used to remove ringing artifacts" help="Select '0' to skip this filter." argument="--ringing-threshold" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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149 </section>
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150 <param name="delimiter" type="hidden" value="tab" argument="--delimiter" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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151 </inputs>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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152 <outputs>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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153 <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peaklists (HDF5 file)" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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154 <data name="report" format="txt" label="${tool.name} on ${on_string}: Report" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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155 <collection name="peaklists_txt" type="list" label="${tool.name} on ${on_string}: Peaklists">
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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156 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tsv" directory="." visible="false" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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157 </collection>
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158
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159 </outputs>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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160 <tests>
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161 <test>
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162 <param name="input|format" value="zip_file" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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163 <param name="input|source" value="MTBLS79_mzml_triplicates.zip" ftype="zip" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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164 <param name="filelist" value="filelist_mzml_triplicates.txt" ftype="tsv" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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165 <param name="function" value="median" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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166 <param name="snr_threshold" value="10.0" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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167 <param name="mults|ppm" value="2.0" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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168 <param name="mults|min_scans" value="1" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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169 <param name="mults|min_fraction" value="0.5" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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170 <param name="mults|rsd_threshold" value="0" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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171 <param name="delimiter" value="tab" />
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172 <output name="hdf5_file_out" value="pls.h5" ftype="h5" compare="sim_size" />
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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173 <output name="report" value="report_pls_01.xt" ftype="txt"/>
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174 <output_collection name="peaklists_txt" type="list">
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175 <element name="batch04_QC17_rep01_262" file="batch04_QC17_rep01_262.txt" ftype="tsv"/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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176 <element name="batch04_QC17_rep02_263" file="batch04_QC17_rep02_263.txt" ftype="tsv"/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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177 <element name="batch04_QC17_rep03_264" file="batch04_QC17_rep03_264.txt" ftype="tsv"/>
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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178 </output_collection>
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179 </test>
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180 <test>
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181 <param name="input|format" value="zip_file" />
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182 <param name="input|source" value="batch_04_QC18_mzml_triplicate.zip" ftype="zip" />
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183 <param name="function" value="median" />
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184 <param name="snr_threshold" value="10.0" />
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185 <param name="mults|ppm" value="2.0" />
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186 <param name="mults|min_scans" value="1" />
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187 <param name="mults|min_fraction" value="0.8" />
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188 <param name="mults|rsd_threshold" value="20.0" />
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189 <param name="delimiter" value="tab" />
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190 <output name="hdf5_file_out" value="pls_QC18.h5" ftype="h5" compare="sim_size"/>
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191 <output name="report" value="report_pls_02.xt" ftype="txt"/>
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192 <output_collection name="peaklists_txt" type="list">
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193 <element name="batch04_QC18_rep01_280" file="batch04_QC18_rep01_280.txt" ftype="tsv"/>
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194 <element name="batch04_QC18_rep02_281" file="batch04_QC18_rep02_281.txt" ftype="tsv"/>
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195 <element name="batch04_QC18_rep03_282" file="batch04_QC18_rep03_282.txt" ftype="tsv"/>
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196 </output_collection>
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197 </test>
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198 </tests>
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199 <help>
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200 -------------
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201 Process Scans
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202 -------------
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203
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204 Description
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205 -----------
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206
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207 | Use this tool to generate a Peaklist for each of the files specified in the filelist. This tool is known to work with Thermo scientific .raw files and with .mzML files.
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208 |
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209 | Peaks are removed from final Peaklist if:
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210
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211 1) they occur in fewer than the user-defined 'Number of technical replicates a peak has to be present in' and/or
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212 2) the relative standard deviation (measured in % and also termed the coefficient of variation) among intensity values for a peak is greater than the user-defined value.
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213
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214 Parameters
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215 ----------
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216
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217 **\1. Source for the dataset**
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218
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219 - **Zip file from history** - use this option if you have uploaded a .zip directory containing ONLY your .mzML or .raw data files
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220
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221 - **Library directory name** - use this option to select data files stored on a data server (e.g. the Research Data Storage at the University of Birmingham).
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222 | In the 'Library directory' box that appears on selecting this option, insert a string specifying the path to your data.
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223 | Ensure to exclude the drive letter and user name, and to separate sub-directories using FORWARD SLASHES e.g. '[Y:\\users\\USERNAME]\\my_study_folder\\my_data_folder' becomes 'my_study_folder/my_data_folder'.
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224
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225 - **Data collection** - this option will provide a drop-down box in which you may select one of the data collections from your current history.
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226
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227 - **Single .mzML or .raw file** - use this option if you have uploaded a single .mzML or .raw file to the current Galaxy history
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228
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229 **\2. Filelist / Samplelist** (HIGHLY RECOMMENDED)
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230
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231 | A tabular-formatted .txt file with columns: filename, replicate, batch, classLabel, injectionOrder.
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232 | Additional collumns are allowed but are not used during processing.
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233 | This file must be uploaded in to (or available from) the current history in order to allow for it to be selected from the drop-down menu.
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234 |
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235
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236 @example_filelist@
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237
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238 **\3. Function to calculate the noise from each scan** (REQUIRED)
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239
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240 Select one option from the drop-down menu to indicate you prefer for noise calculation algorithm - median, mean, mean absolute deviation and 'Xcalibur' (i.e. noise values as displayed in Thermo Xcalibur software will be used) are the valid options.
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241
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242 **\4. Signal-to-noise ratio threshold** (REQUIRED)
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243
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244 A numerical value from 0 upwards. Peaks with signal-to-noise ratios less-than or equal to this value will be removed from output Peaklist.
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245
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246 **\5. Filter specific scan windows or scan events?** (OPTIONAL)
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247
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248 | A boolean toggle ('No' = do not perform scan event filtering; 'Yes' = filter specific scan events)
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249 | When 'Yes' is selected, users must specify whether to 'Exclude' or 'Include' specific scan events.
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250
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251 Users must then:
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252
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253 - Click the '+ Description' button and insert the 'Start m/z for scan event' and 'Stop m/z for scan event' for the scan event to be excluded or included.
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254 - Select the 'scan type' to be filtered from 'Full scan' or 'SIM scan'
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255 - Click '+ Description' to 'Exclude/Include' an additional scan event
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256
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257 **\6. Show options for multiple scans**
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258
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259 - **Minimum number of scans required for each m/z window or scan event** - A numerical value from 1 upwards to specify the number of instances of a given scan event required in order to peaks in this scan event to be included in the output Peaklist.
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260 - **ppm error tolerance** - A numerical value from 0 upwards. This option serves to define the maximum allowable difference in m/z values (measured in parts-per-million) for mass spectral peaks to be clustered across replicates of the same scan event.
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261 - **Minimum fraction (i.e. percentage) of scans a peak has to be present in** - A numerical value specifying the minimum number of scans a given mass spectral peak must be present in for it to be kept in the output Peaklist. The ppm error specified by the user will significantly impact which peaks fulfil this criteria.
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262
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263 **\7. Show advanced options**
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264
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265 - **Skip SIM-stitching** (REQUIRED; default = 'NO')
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266
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267 | A boolean toggle ('No' = perform SIM stitching; 'Yes' = skip stitching procedure)
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268 | When set to 'yes' it will skip the processing step where (SIM) windows are 'stitched' or 'joined' together.
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269 | Set this option to 'yes' if you like to proces individual scan/SIM windows (events/ranges) without 'stitching' them.
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270
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271 - **Remove m/z range(s)** (OPTIONAL)
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272
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273 This option allow specific regions of the output peak matrices to be deleted by the user - this option may be useful for removing sections of a spectrum known to correspond to system noise peaks.
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274
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275 - **Start m/z of removal range** - a numerical value corresponding to the lowest m/z value in the spectral region to be removed
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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276 - **End m/z of removal range** - a numerical value corresponding to the highest m/z value in the spectral region to be removed
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277
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278 - **Relative intensity threshold used to remove ringing artefacts** (OPTIONAL)
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279
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280 - Fourier transform-based mass spectra often contain many peaks (ringing artefacts) around spectral features corresponding to genuine bio-molecules.
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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281 - A numerical value indicating the required relative intensity a peak must exceed (with reference to the largest peak in a cluster of peaks) in order to be retained.
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282
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283 Output file(s)
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284 --------------
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285
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286 | A HDF5 file containing the processed Peaklists
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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287 |
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288 | A processed Peaklist, in .tsv format, for each file specified in the filelist (Data Collection)
d129e75a31d9 planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit d30de6d202e1b97aaca189acc612ae87e95d033f
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289
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290 - Tab-delimited text file containing a numeric data matrix, with . as decimal, and NA for missing values.
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291 - Includes additional information, such as the signal-to-noise ratio, relative-standard deviation (rsd) and 'purity' for each peak.
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292
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293 @github_developers_contributors@
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294
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295 </help>
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296
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297 <expand macro="citations" />
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298 </tool>