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annotate myrimatch.xml @ 6:ea7872c231de draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit e28e65d5554b851fa7880f0bfe32870524852276"
author galaxyp
date Fri, 12 Jun 2020 10:56:23 -0400
parents e26ef51ef341
children
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1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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1 <tool id="myrimatch" version="@VERSION@.0" name="MyriMatch">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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2 <description>Identify peptides in tandem mass spectra.</description>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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3 <macros>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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4 <import>macros.xml</import>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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5 </macros>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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6 <expand macro="requirements" />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Job Failed" />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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9 <regex match="^Could not find the default configuration file.*$"
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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10 source="both"
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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11 level="warning" />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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12 </stdio>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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13 <command>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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14 <![CDATA[
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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15 #set $db_name = $ProteinDatabase.display_name.replace(".fasta", "") + ".fasta"
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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16 #if $OutputFormat.value == "mzIdentML"
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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17 #set $output_ext="mzid"
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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18 #else
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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19 #set $output_ext="pepXML"
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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20 #end if
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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21 #set $input_name = $input.display_name
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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22 #set $output_name = $input_name.split(".")[0] + "." + $output_ext
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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23
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24 #set $static_mods_str = ""
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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25 #for $static_mod in $StaticMods
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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26 #set $static_mods_str = $static_mods_str + " " + str($static_mod.aa) + " " + str($static_mod.mass)
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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27 #end for
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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28 #set $static_mods_str = $static_mods_str.lstrip()
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29
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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30 #set $dynamic_mods_str = ""
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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31 #for $dynamic_mod in $DynamicMods
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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32 #set $dynamic_mods_str = $dynamic_mods_str + " " + str($dynamic_mod.motif) + " * " + str($dynamic_mod.mass)
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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33 #end for
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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34 #set $dynamic_mods_str = $dynamic_mods_str.lstrip()
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35
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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36 ln -s '$input' '${input_name}' &&
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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37 ln -s '$ProteinDatabase' '${db_name}' &&
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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38 myrimatch -DecoyPrefix '${DecoyPrefix}' -cpus \${GALAXY_SLOTS:-1}
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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39 -ProteinDatabase '${db_name}'
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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40 -OutputFormat '${OutputFormat}'
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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41 '${input_name}'
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42 -StaticMods '${static_mods_str}'
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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43 -DynamicMods '${dynamic_mods_str}'
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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44 -MaxDynamicMods $MaxDynamicMods
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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45 -CleavageRules '${CleavageRules}'
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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46 -MinTerminiCleavages $MinTerminiCleavages
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47 -MaxMissedCleavages $MaxMissedCleavages
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48 #set $precursor_type = $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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49 -PrecursorMzToleranceRule '${tolerance_options.precursor_tolerance.PrecursorMzToleranceRule}'
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50 #if $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule == "auto" or $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule == "mono"
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51 -MonoPrecursorMzTolerance '${tolerance_options.precursor_tolerance.MonoPrecursorMzTolerance}${tolerance_options.precursor_tolerance.mono_precursor_mz_tolerance_units}'
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52 #end if
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53 #if $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule == "auto" or $tolerance_options.precursor_tolerance.PrecursorMzToleranceRule == "avg"
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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54 -AvgPrecursorMzTolerance '${tolerance_options.precursor_tolerance.AvgPrecursorMzTolerance}${tolerance_options.precursor_tolerance.avg_precursor_mz_tolerance_units}'
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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55 #end if
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56 -FragmentMzTolerance '${tolerance_options.FragmentMzTolerance}${tolerance_options.fragment_mz_tolerance_units}'
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57 -UseSmartPlusThreeModel $advanced.UseSmartPlusThreeModel
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58 -MinPeptideLength $advanced.MinPeptideLength
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59 -MaxPeptideLength $advanced.MaxPeptideLength
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60 -NumChargeStates $advanced.NumChargeStates
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61 -MaxResultRank $advanced.MaxResultRank
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62 #set $set = str($advanced.MonoisotopeAdjustmentSet).replace("[[", "[").replace("]]","]")
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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63 -MonoisotopeAdjustmentSet '$set'
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64 #if $advanced.MaxPeakCount
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65 -MaxPeakCount $advanced.MaxPeakCount
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66 #end if
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67 #if $advanced.fragmentation_rule.FragmentationAutoRule
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68 -FragmentationAutoRule false -FragmentationRule 'manual:${advanced.fragmentation_rule.FragmentationRule}'
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69 #end if
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70 &&
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71 mv '$output_name' output
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72 ]]>
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73 </command>
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74 <inputs>
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75 <param name="input" type="data" format="mzml,mzxml,mgf,ms2,mz5" label="Input Raw MS File(s)"/>
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76 <param argument="-OutputFormat" type="select" label="Output Type" help="The file format to use for results of the search.">
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77 <option value="pepXML">pepXML</option>
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78 <option value="mzIdentML">mzIdentML</option>
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79 </param>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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80 <param argument="-ProteinDatabase" format="fasta" type="data" label="Protein Database" help="The FASTA protein database to search against. Only amino-acid type FASTA is supported." />
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81 <param argument="-DecoyPrefix" type="text" label="Decoy Prefix" value="rev_" help="If the protein database contains accessions prefixed with this string, those proteins will be considered decoys. If there are no decoy protein, this prefix will be used to generate an automatic decoy for each target protein. Set this to an empty string to disable automatic decoys." />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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parents:
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82 <param argument="-CleavageRules" type="select" label="Cleavage Agent" help="The cleavage agent to generate in silico peptides from the protein database." >
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
83 <option value="Trypsin/P">Trypsin/P (allows for cut after K or R)</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
84 <option value="Trypsin">Trypsin (normal trypsin cut, disallows cutting when the site is before a proline)</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
85 <option value="Chymotrypsin">Chymotrypsin (allows cut after F,Y,W,L. Disallows cutting before proline)</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
86 <option value="TrypChymo">TrypChymo (combines "Trypsin/P" and "Chymotrypsin" cleavage rules)</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
87 <option value="Lys-C">Lys-C</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
88 <option value="Lys-C/P">Lys-C/P (Lys-C, disallowing cutting before proline)</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
89 <option value="Asp-N">Asp-N</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
90 <option value="PepsinA">PepsinA (cuts right after F, L)</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
91 <option value="CNBr">CNBr (cyanogen bromide)</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
92 <option value="Formic_acid">Formic acid</option>
5
e26ef51ef341 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot commit 443a91ed5ca98c92635897f670b8f4efda51c78d
galaxyp
parents: 1
diff changeset
93 <option value="Glu-C">Glu-C (glutamyl endopeptidase)</option>
1
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
94 </param>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
95 <param argument="-MinTerminiCleavages" type="select" label="Cleavage Specificity" help="Controls which peptide termini must match the cleavage rules.">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
96 <option value="2">Fully specific (both termini match cleavage rules)</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
97 <option value="1" selected="true">Semi-specific (at least one terminus must match cleavage rules)</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
98 <option value="0">Non-specific (neither terminus is required to match cleavage rules)</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
99 </param>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
100 <param argument="-MaxMissedCleavages" type="integer" min="0" value="2" label="Maximum Missed Cleavages" help="Candidate peptides with more than this number of uncleaved cleavage sites will be skipped." />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
101 <repeat name="StaticMods" title="Static Modifications" help="Modifications that are always applied to an amino acid. (-StaticMods)">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
102 <param name="aa" type="text" label="Amino Acid">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
103 <sanitizer><valid initial="string.ascii_uppercase"><remove value="B"/><remove value="J"/><remove value="O"/><remove value="Z"/></valid></sanitizer>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
104 </param>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
105 <param name="mass" type="float" label="Mass" value="0" />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
106 </repeat>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
107 <repeat name="DynamicMods" title="Dynamic Modifications" help="Modifications that can either be present or absent on an amino acid. (-DynamicMods)">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
108 <param name="motif" type="text" label="Amino Acid Motif">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
109 <sanitizer>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
110 <valid initial="string.ascii_uppercase">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
111 <remove value="B"/><remove value="J"/><remove value="O"/><remove value="Z"/>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
112 <add value="["/><add value="]"/>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
113 <add value="("/><add value=")"/>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
114 <add value="{"/><add value="}"/>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
115 <add value="."/>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
116 <add value="!"/>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
117 </valid>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
118 </sanitizer>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
119 </param>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
120 <param name="mass" type="float" label="Mass" value="0" />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
121 </repeat>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
122 <param argument="-MaxDynamicMods" type="integer" min="0" value="4" label="Maximum Dynamic Mods" help="Candidate peptides with more than this number of dynamic modifications will be skipped." />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
123 <section name="tolerance_options" title="M/Z Tolerance Options" expanded="True">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
124 <conditional name="precursor_tolerance">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
125 <param argument="-PrecursorMzToleranceRule" type="select" label="Precursor Mass Type" help="For data from Thermo instruments, using the 'auto' setting on a will automatically choose monoisotopic or average mass values, for other instruments monoisotopic or average should be chosen.">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
126 <option value="auto">Auto</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
127 <option value="avg">Average</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
128 <option value="mono">Monoisotopic</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
129 </param>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
130 <when value="auto">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
131 <param argument="-MonoPrecursorMzTolerance" type="float" min="0.000001" value="10" label="Monoisotopic Precursor m/z Tolerance" help="This tolerance will be used for spectra that are determined to have monoisotopic precursors. MonoisotopeAdjustmentSet is applied to these." />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
132 <param name="mono_precursor_mz_tolerance_units" type="select" label="Monoisotopic Precursor m/z Tolerance Units">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
133 <option value="ppm">Parts per million</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
134 <option value="daltons">Daltons</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
135 </param>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
136 <param argument="-AvgPrecursorMzTolerance" type="float" min="0.000001" value="1.25" label="Average Precursor m/z Tolerance" help="This tolerance will be used for spectra that are determined to have average mass precursors. MonoisotopeAdjustmentSet is not applied to these." />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
137 <param name="avg_precursor_mz_tolerance_units" type="select" label="Average Precursor m/z Tolerance Units">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
138 <option value="ppm">Parts per million</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
139 <option value="daltons" selected="true">Daltons</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
140 </param>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
141 </when>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
142 <when value="avg">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
143 <param argument="-AvgPrecursorMzTolerance" type="float" min="0.000001" value="1.25" label="Average Precursor m/z Tolerance" help="This tolerance will be used for all spectra, but MonoisotopeAdjustmentSet will never be applied." />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
144 <param name="avg_precursor_mz_tolerance_units" type="select" label="Average Precursor m/z Tolerance Units">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
145 <option value="ppm">Parts per million</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
146 <option value="daltons" selected="true">Daltons</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
147 </param>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
148 </when>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
149 <when value="mono">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
150 <param argument="-MonoPrecursorMzTolerance" type="float" min="0.000001" value="10" label="Monoisotopic Precursor m/z Tolerance" help="This tolerance will be used for all spectra, and MonoisotopeAdjustmentSet is likewise applied to all spectra." />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
151 <param name="mono_precursor_mz_tolerance_units" type="select" label="Monoisotopic Precursor m/z Tolerance Units">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
152 <option value="ppm">Parts per million</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
153 <option value="daltons">Daltons</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
154 </param>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
155 </when>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
156 </conditional>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
157 <param argument="-FragmentMzTolerance" type="float" min="0.000001" value="0.5" label="Fragment m/z Tolerance" help="This tolerance is used for matching to fragment ions." />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
158 <param name="fragment_mz_tolerance_units" type="select" label="Fragment m/z Tolerance Units">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
159 <option value="ppm">Parts per million</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
160 <option value="daltons" selected="true">Daltons</option>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
diff changeset
161 </param>
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
galaxyp
parents:
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162 </section>
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163 <section name="advanced" title="Advanced Options" expanded="False">
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164 <param argument="-MaxPeakCount" type="integer" min="10" value="" optional="true" label="Use Max Peaks" help="Filter out all but the specified number of peaks, keep empty to use all peaks." />
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165 <conditional name="fragmentation_rule">
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166 <param argument="-FragmentationAutoRule" type="boolean" label="Override Fragmentation Rule (Ion Series)" help="If the input file provides mass analyzer information (mzML, mzXML, mz5), MyriMatch can automatically choose the ion series to search on a scan-by-scan basis." />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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167 <when value="false" />
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168 <when value="true">
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169 <param argument="-FragmentationRule" type="text" label="Fragmentation Rule" help="Specify as a comma-separated list of a, b, c, x, y, z, or z* (z+1), e.g. 'b,y,z'" />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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170 </when>
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171 </conditional>
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172 <param argument="-MinPeptideLength" type="integer" min="3" value="5" label="Minimum Peptide Length" help="Candidate peptides shorter than this will not be compared against any spectrum." />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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173 <param argument="-MaxPeptideLength" type="integer" min="3" value="75" label="Maximum Peptide Length" help="Candidate peptides longer than this will not be compared against any spectrum." />
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174 <param argument="-UseSmartPlusThreeModel" type="boolean" truevalue="true" falsevalue="false" label="Use Smart Plus 3 Model" help="For +3 and higher precursors, the fragment ions predicted depend on the way this parameter is set. When this parameter is true, then for each peptide bond, an internal calculation is done to estimate the basicity of the b and y fragment sequence. When this parameter is false, however, ALL possible charge distributions for the fragment ions are generated for every peptide bond." checked="true" />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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175 <param argument="-NumChargeStates" type="integer" min="1" value="3" label="Number of Charge States" help="For spectra with an ambiguous multiple charge state, it will be treated as any charge in the range: [+2,NumChargeStates]." />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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176 <param argument="-MaxResultRank" type="integer" min="1" value="2" label="Maximum Result Rank" help="The maximum rank of a search result (results with the same score occupy the same rank)." />
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177 <param argument="-MonoisotopeAdjustmentSet" type="text" value="[-1,2]" label="Monoisotope Adjustment Set" help="For monoisotopic precursors where the monoisotope may have been incorrectly assigned to a nearby isotope, this range of adjustments will be considered. Instead of trying a wide precursor tolerance for a spectrum, this tries multiple tight tolerances.">
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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178 <sanitizer invalid_char=""><valid initial="string.digits"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer>
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179 </param>
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180 </section>
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181 </inputs>
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182 <outputs>
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183 <data format="raw_pepxml" name="output" from_work_dir="output">
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184 <change_format>
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185 <when input="OutputFormat" value="mzIdentML" format="mzid" />
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186 </change_format>
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187 </data>
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188 </outputs>
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189 <tests>
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190 <test>
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191 <param name="input" value="input/201208-378803.mzML" />
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192 <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
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193 <param name="DecoyPrefix" value="XXX_" />
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194 <param name="StaticMods_0|aa" value="C" />
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195 <param name="StaticMods_0|mass" value="58.00548" />
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196 <param name="DynamicMods_0|motif" value="M" />
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197 <param name="DynamicMods_0|mass" value="15.9949" />
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198 <param name="DynamicMods_1|motif" value="(Q" />
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199 <param name="DynamicMods_1|mass" value="-17.026" />
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200 <param name="DynamicMods_2|motif" value="[QN]" />
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201 <param name="DynamicMods_2|mass" value="0.984016" />
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202 <param name="PrecursorMzToleranceRule" value="mono" />
1881935e5351 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
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203 <param name="MonoPrecursorMzTolerance" value="50" />
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204 <param name="MinTerminiCleavages" value="1" />
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205 <param name="MaxMissedCleavages" value="2" />
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206 <param name="MaxDynamicMods" value="2" />
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207 <param name="NumChargeStates" value="5" />
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208 <param name="MaxResultRank" value="3" />
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209 <param name="MonoisotopeAdjustmentSet" value="[-1,2]" />
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210 <param name="UseSmartPlusThreeModel" value="false" />
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211 <output name="output" file="201208-378803-mm.pepXML" lines_diff="9000" />
1
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212 </test>
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213 <test>
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214 <param name="input" value="input/201208-378803.mzML" />
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215 <param name="ProteinDatabase" value="input/cow.protein.PRG2012-subset.fasta" />
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216 <param name="CleavageRules" value="Trypsin" />
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217 <param name="DecoyPrefix" value="XXX_" />
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218 <param name="PrecursorMzToleranceRule" value="mono" />
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219 <param name="MonoPrecursorMzTolerance" value="15" />
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220 <param name="MinTerminiCleavages" value="2" />
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221 <param name="MaxMissedCleavages" value="4" />
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222 <param name="NumChargeStates" value="3" />
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223 <param name="MaxResultRank" value="1" />
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224 <param name="MonoisotopeAdjustmentSet" value="0" />
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225 <output name="output" file="201208-378803-mm-15ppm-fully-tryptic.pepXML" lines_diff="200" />
1
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226 </test>
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227 </tests>
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228 <help>
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229 <![CDATA[
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230 **What it does**
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231
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232 Performs protein identification via database search using MyriMatch.
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233 ]]>
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234 </help>
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235 <citations>
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236 <citation type="doi">10.1021/pr0604054</citation>
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237 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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238 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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239 </citations>
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240 </tool>