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annotate metfrag.xml @ 0:75c805123b45 draft

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planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
author tomnl
date Tue, 24 Jul 2018 07:59:44 -0400
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0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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1 <tool id="metfrag" name="MetFrag" version="0.1.3">
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2 <description> </description>
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3 <requirements>
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4 <requirement type="package" version="2.4.2">metfrag</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 #set $tool_directory = $getVar('__tool_directory__', '../../../../tools/msmstools')
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9 python $tool_directory/metfrag.py
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10 --input "$input"
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11 --db_local '$db_local'
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12 --db_online '$db_online'
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13 --ppm $ppm
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14 --ppm_frag $ppm_frag
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15 --fragmasstol $fragmasstol
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16 --polarity $polarity
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17 --results '$results'
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18 --threads \${GALAXY_SLOTS:-4}
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19 ]]></command>
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20 <inputs>
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21 <param name="input" type="data" format="msp,txt" label="MSP file (Output from Create MSP tool)" argument="--input"/>
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22 <param name="db_local" type="data" format="csv" optional="true" label="Local Database (CSV)" argument="--db_local"/>
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23 <param name="db_online" type="select" optional="true" label="Available MetFrag Databases" argument="--db_online">
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24 <option value="PubChem" selected="true">PubChem</option>
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25 <option value="KEGG">KEGG</option>
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26 <option value="ChemSpider">ChemSpider</option>
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27 </param>
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28 <param name="ppm" type="integer" value="10" label="Relative Mass Deviation" argument="--ppm"/>
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29 <param name="ppm_frag" type="integer" value="5" label="Fragment Peak Match Relative Mass Deviation" argument="--ppm_frag"/>
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30 <param name="fragmasstol" type="float" value="0.001" label="Fragment Peak Match Absolute Mass Deviation" argument="--fragmasstol"/>
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31 <param name="polarity" type="select" label="Ion Mode" argument="--polarity">
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32 <option value="pos" selected="true">Positive</option>
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33 <option value="neg">Negative</option>
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34 </param>
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35 </inputs>
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36 <outputs>
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37 <data name="results" format="tabular" label="${tool.name} results of ${input.name}" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input" value="input.msp"/>
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42 <param name="db_local" value="demo_db.csv"/>
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43 <output name="results" file="metfrag.tabular"/>
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44 </test>
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45 </tests>
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46 <help>
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47 -------
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48 MetFrag
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49 -------
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50
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51 Description
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52 -----------
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53
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54 MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecule's structure. Candidate molecules of different databases are fragmented "in silico" and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment.
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55
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56 Website: http://c-ruttkies.github.io/MetFrag
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57
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58 Parameters
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59 ----------
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60
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61 **\1. MSP file**
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62
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63 MSP file created using *Create MSP* tool
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64
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65 **\2a. Local Database (CSV)**
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66
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67 Custom database file in CSV format with the following structure:
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68
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69 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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70 | Identifier | MonoisotopicMass | SMILES | InChI | Name |...|
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71 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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72 | HMDB0000123 | 75.03202841 | NCC(O)=O | InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) | Glycine |...|
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73 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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74 | HMDB0002151 | 78.0139355 | CS(C)=O | InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 | Dimethyl sulfoxide |...|
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75 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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76 | ... | ... | ... | ... | ... |...|
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77 +-------------+------------------+----------+---------------------------------------------+----------------------+---+
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78
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79
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80 Table continued:
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81
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82 +---+------------------+-----------------------------+------------------+------------+-------------+
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83 |...| MolecularFormula | InChIKey | InChIKey1 | InChIKey2 | InChIKey3 |
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84 +---+------------------+-----------------------------+------------------+------------+-------------+
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85 |...| C2H5NO2 | DHMQDGOQFOQNFH-UHFFFAOYSA-N | DHMQDGOQFOQNFH | UHFFFAOYSA | N |
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86 +---+------------------+-----------------------------+------------------+------------+-------------+
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87 |...| C2H6OS | IAZDPXIOMUYVGZ-UHFFFAOYSA-N | IAZDPXIOMUYVGZ | UHFFFAOYSA | N |
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88 +---+------------------+-----------------------------+------------------+------------+-------------+
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89 |...| ... | ... | ... | ... | ... |
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90 +---+------------------+-----------------------------+------------------+------------+-------------+
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93 **\2b. Online Database**
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94
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95 * PubChem
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96
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97 * KEGG
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98
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99 * ChemSpider
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100
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101 **\3. Relative Mass Deviation in PPM**
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102
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103 **\4. Fragment Peak Match Relative Mass Deviation in PPM**
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104
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105 **\5. Fragment Peak Match Absolute Mass Deviation in Da**
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106
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107 **\6. Ion Mode**
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108
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109 * Positive
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110
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111 * Negative
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112
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113
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114 Developers and contributors
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115 ---------------------------
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116
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117 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
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118 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
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119
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120 </help>
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121 <citations>
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122 <citation type="doi">10.1186/s13321-016-0115-9</citation>
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123 </citations>
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124 </tool>