Mercurial > repos > computational-metabolomics > mspurity_createdatabase

annotate createDatabase.xml @ 4:3d36a391612c draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
author computational-metabolomics
date Mon, 10 Aug 2020 08:41:22 -0400
parents 19fd19059791
children 2f71b3495221
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1 <tool id="mspurity_createdatabase" name="msPurity.createDatabase" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
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2 <description>Create and SQLite database of an LC-MS(/MS) experiment</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$__tool_directory__/createDatabase.R'
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9 --outDir=.
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10 --xset_xa='$xset_xa'
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11 --pa='$pa'
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12 --xcms_camera_option=$camera_xcms
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13 --cores=\${GALAXY_SLOTS:-4}
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14 #if $file_load_conditional.file_load_select=="yes"
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15 --mzML_files='
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16 #for $i in $file_load_conditional.input
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17 $i,
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18 #end for
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19 '
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20 --galaxy_names='
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21 #for $i in $file_load_conditional.input
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22 $i.name,
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23 #end for
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24 '
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25 #end if
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26
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27 #if $eic
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28 --eic
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29 #end if
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30
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31 #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
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32 --grpPeaklist='$grp_peaklist'
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33 #end if
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34
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35 ]]></command>
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36 <inputs>
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37 <param argument="--xset_xa" type="data" label="xcmsSet or CAMERA object"
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38 help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file.
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39 Please specify which to use below"
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40 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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41 <expand macro="camera_xcms" />
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42 <param argument="--pa" type="data" label="purityA object (frag4feature output)" format="rdata"
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43 help="purityA object saved as 'pa' in a RData file (output from frag4feature)"/>
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44 <param argument="--eic" type="boolean" label="Include EIC data?"
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45 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
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46 the database. Note, this will take considerable time for large datasets and
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47 the resulting SQLite database can be large"/>
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48 <expand macro="grp_peaklist" />
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49 <expand macro="fileload" />
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50 </inputs>
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51 <outputs>
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52 <data name="createDatabase_output_sqlite" format="sqlite"
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53 label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
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54 from_work_dir="createDatabase_output.sqlite" />
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55
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56 </outputs>
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57 <tests>
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58 <test>
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59 <conditional name="file_load_conditional">
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60 <param name="file_load_select" value="yes"/>
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61 <param name="input" >
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62 <collection type="list">
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63 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
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64 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
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65 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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66 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
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67 </collection>
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68 </param>
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69 </conditional>
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70 <param name="camera_xcms" value="xcms"/>
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71 <param name="xset_xa" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
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72 <param name="pa" value="averageFragSpectra_output_all.RData"/>
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73 <output name="createDatabase_output_sqlite" value="createDatabase_output.sqlite" ftype="sqlite" compare="sim_size"/>
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74 </test>
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75
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76 <test>
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77 <conditional name="file_load_conditional">
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78 <param name="file_load_select" value="yes"/>
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79 <param name="input" >
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80 <collection type="list">
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81 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
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82 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
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83 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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84 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
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85 </collection>
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86 </param>
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87 </conditional>
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88 <param name="camera_xcms" value="xcms"/>
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89 <param name="eic" value="true"/>
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90 <param name="xset_xa" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
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91 <param name="pa" value="averageFragSpectra_output_all.RData"/>
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92 <output name="createDatabase_output_sqlite" value="createDatabase_output_eic.sqlite" ftype="sqlite" compare="sim_size"/>
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93 </test>
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94 </tests>
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95
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96 <help><![CDATA[
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97 =============================================================
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98 Create SQLite database for LC-MS(/MS) dataset
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99 =============================================================
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100 ** General **
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101
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102 Create and SQLite database of an LC-MS(/MS) experiment (replaces the create_database function).
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103
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104 Schema details can be found [here](https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-datatabase-schema.html).
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105
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106 **Example LC-MS/MS processing workflow**
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107
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108 * Purity assessments
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109 + (mzML files) -> purityA -> (pa)
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110 * XCMS processing
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111 + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
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112 * Fragmentation processing
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113 + (xset, pa) -> frag4feature -> filterFragSpectra -> averageAllFragSpectra -> **createDatabase** -> spectralMatching -> (sqlite spectral database)
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114
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115
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116 -----------
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117 Output
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118 -----------
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119 * lcms_sqlite: An SQLite database of the LC-MS(/MS) data (including fragmentation scans)
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120
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121 ]]></help>
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122 <expand macro="citations" />
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123 </tool>