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annotate cameradims.xml @ 15:4fc58ee7dd62 draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 9c1dec94a397a8c34b10f0fe35df4159daf53ae3-dirty
author tomnl
date Wed, 20 Jun 2018 16:17:36 -0400
parents 429f65a5a373
children ec2283d81c6a
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15
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1 <tool id="cameradims" name="CAMERA_DIMS" version="0.2.1">
0
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2 <description>Modification of the R package CAMERA to work on DIMS data</description>
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3 <requirements>
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4 <requirement type="package" version="0.2.6">r-cameradims</requirement>
0
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5 <requirement type="package" version="1.4.4" >r-optparse</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command interpreter="Rscript"><![CDATA[
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11 cameradims.R --in_file $peaks_file
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12 --out_dir .
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13 --ppm_adduct $ppm_adduct
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14 --ppm_iso $ppm_iso
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15 --mzabs_adduct $mzabs_adduct
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16 --mzabs_iso $mzabs_iso
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17 --maxiso $maxiso
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18 --maxcharge $maxcharge
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19 --maxmol $maxmol
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20 --polarity $polarity
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21 --rule_type $ruleset.ruleset
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22 #if $ruleset.ruleset == 'user'
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23 --rule_path $ruleset.rulesfile
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24 #end if
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25 #if $export_ruleset
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26 --export_ruleset
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27 #end if
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28 --intensity_filter=$intensity_filter
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29 ]]></command>
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30
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31 <inputs>
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32 <param type="data" name="peaks_file" format="tabular,tsv"
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33 help="tsv or tabular file with mz and intensity columns"/>
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34 <param name="ppm_adduct" type="float" label="ppm (adduct)" value="5"
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35 help="general ppm error (adduct)"/>
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36 <param name="ppm_iso" type="float" label="ppm (iso)" value="5"
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37 help="general ppm error (iso)"/>
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38 <param name="mzabs_adduct" type="float" label="mzabs (adduct)" value="0.015"
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39 help="general absolute error in m/z"/>
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40 <param name="mzabs_iso" type="float" label="mzabs (iso)" value="0.015"
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41 help="general absolute error in m/z"/>
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42 <param name="maxmol" type="integer" label="maxmol" value="3"
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43 help="highest number(n) of allowed clusterion [nM+ion] (argument called multiplier in findAdducts())"/>
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44 <param name="maxiso" type="integer" label="maxiso" value="4"
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45 help="max number of expected isotopes"/>
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46 <param name="maxcharge" type="integer" label="maxcharge" value="3"
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47 help="max ion charge for finding isotopes"/>
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48 <param name="polarity" type="select" label="polarity" help="Which polarity mode was used for measuring of the ms sample" >
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49 <option value="pos" selected="true">positive</option>
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50 <option value="neg">negative</option>
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51 </param>
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52
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53 <param name="intensity_filter" type="float" label="Intensity filter" value="5000"
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54 help="Filter out any peaks that have intensity less than this value. (Adduct calculation may take
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55 a very long time if peaks are not filtered before hand) "/>
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56
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57 <conditional name="ruleset">
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58 <param name="ruleset" type="select" label="Rules for adducts" >
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59 <option value="primary adducts" >Primary adducts ([M+Na]+, [M+K]+ and [M+NH4]+")</option>
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60 <option value="extended" selected="true" >Extended adducts</option>
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61 <option value="extended_large" >Extended adducts (large)</option>
0
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62 <option value="user" >Provide a csv file of the rules to use</option>
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63 </param>
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64 <when value="user">
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65 <param type="data" name="rulesfile" format="tsv, tabular"
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66 help="User supplied rules file used to to calculate adducts, should contain the following
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67 columns name,nmol,charge,massdiff,oidscore,quasi,ips.
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68 If using the adducts to guide fragmentation then the frag_score column should be included. Where
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69 a score of 1 indicates the adduct is the best adduct form to fragment"/>
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70 </when>
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71 <when value="extended">
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72 </when>
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73 <when value="primary adducts">
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74 </when>
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75 </conditional>
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76 <param name="export_ruleset" type="boolean" label="Export the adduct ruleset used?" help=""/>
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77 </inputs>
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78 <outputs>
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79 <data name="camera_annotated_map" format="tsv" label="${tool.name} on ${on_string}: map"
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80 from_work_dir="camera_annotated_map.txt" />
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81 <data name="camera_annotated_peaklist" label="${tool.name} on ${on_string}: peaklist"
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82 from_work_dir="camera_annotated_peaklist.txt" format="tsv"/>
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83 <data name="ruleset" label="${tool.name} on ${on_string}: ruleset"
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84 from_work_dir="ruleset.txt" format="tsv">
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85 <filter>export_ruleset is True</filter>
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86 </data>
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87
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88
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89
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="peaks_file" value="peaklist_in.tsv" ftype="tsv"/>
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94 <output name="camera_annotated_peaklist" value="camera_annotated_peaklist.txt"/>
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95 <output name="camera_annotated_map" value="camera_annotated_map.txt"/>
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96 </test>
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97 </tests>
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98 <help><![CDATA[
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99 cameraDIMS
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100
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101 ]]></help>
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102 <citations>
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103 <citation type="doi">10.1021/ac202450g</citation>
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104 </citations>
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105 </tool>