Mercurial > repos > tomnl > create_sqlite_db

annotate create_sqlite_db.xml @ 6:3d8bde261c95 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80
author tomnl
date Mon, 23 Apr 2018 10:16:41 -0400
parents 9ab472c5714c
children c59965822dc8
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1 <tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.4">
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2 <description>
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3 Create SQLite database of an XCMS-CAMERA dataset
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4 </description>
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7 <macros>
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8 <import>macros.xml</import>
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9 </macros>
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11 <expand macro="requirements">
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13 </expand>
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16 <stdio>
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17 <exit_code range="1:" />
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18 </stdio>
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19 <command interpreter="Rscript"><![CDATA[
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20 create_sqlite_db.R
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21 --out_dir=.
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22 --xset_xa=$xset_xa
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23 --pa=$pa
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24 --xcms_camera_option=$camera_xcms
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25 --cores=\${GALAXY_SLOTS:-4}
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26 #if $file_load_conditional.file_load_select=="yes"
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27 --mzML_files='
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28 #for $i in $file_load_conditional.input
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29 $i,
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30 #end for
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31 '
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32 --galaxy_names='
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33 #for $i in $file_load_conditional.input
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34 $i.name,
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35 #end for
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36 '
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37 #end if
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38
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39 #if $eic
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40 --eic
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41 #end if
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42 #if $raw_rt_columns
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43 --raw_rt_columns
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44 #end if
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45 #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
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46 --grp_peaklist=$grp_peaklist
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47 #end if
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48
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49 ]]></command>
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50 <inputs>
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51
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52
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53 <param type="data" name="xset_xa" label="xcmsSet or CAMERA object"
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54 help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file. Please
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55 specify which to use below" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>
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56 <expand macro="camera_xcms" />
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57
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58 <param type="data" name="pa" label="purityA object" format="rdata"
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59 help="purityA object saved as 'pa' in a RData file (output from assess_purity_msms)"/>
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60
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61 <param name="eic" type="boolean" label="Include EIC data?"
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62 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
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63 the database. Note, this will take considerable time for large datasets and
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64 the resulting SQLite database can be large"/>
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65
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66 <param name="raw_rt_columns" type="boolean" label="Use user defined Raw RT columns?"
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67 help="Only use if the track_rt_raw tool has been used"/>
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68
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69
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70 <expand macro="grp_peaklist" />
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71
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72
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73 <expand macro="fileload" />
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74
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75 </inputs>
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76 <outputs>
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77 <data name="lcms_data_sqlite" format="sqlite" label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
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78 from_work_dir="lcms_data.sqlite" />
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79 <data name="cpeakgroup_msms" format="tsv" label="${tool.name} on ${on_string}: c-peak-group-msms"
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80 from_work_dir="cpeakgroup_msms.tsv" />
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81
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82 </outputs>
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83 <tests>
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84 <test>
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85 <conditional name="file_load_conditional">
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86 <param name="file_load_select" value="yes"/>
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87 <param name="input" >
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88 <collection type="list">
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89 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
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90 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
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91 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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92 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
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93 </collection>
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94 </param>
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95 </conditional>
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96 <param name="camera_xcms" value="xcms"/>
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97 <param name="xset_xa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
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98 <param name="pa" value="frag4feature.rdata"/>
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99 <output name="cpeakgroup_msms" value="cpeakgroup_msms.tsv" >
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100
0
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101 </output>
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102 </test>
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103 </tests>
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104
0
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105 <help><![CDATA[
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106 =============================================================
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107 Create SQLite database for LC-MS(/MS) dataset
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108 =============================================================
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109 Create an SQLite database for the msPurity and XCMS (CAMERA) outputs. The SQLite database created can
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110 be used as input to the spectral_matching tool.
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111
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112 Please note that getting the extracted ion chromatograms can take a long time if the dataset has a large number of files and peaks.
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113
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114 -----------
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115 Output
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116 -----------
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117 * lcms_sqlite: An SQLite database of the LC-MS(/MS) data (including fragmentation scans)
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118 * cpeakgroup_msms: A csv file for all grouped features that have associated fragmentation spectra
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119
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120 ]]></help>
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121 <expand macro="citations" />
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122 </tool>