Mercurial > repos > tomnl > mspurity_createdatabase

annotate createDatabase.xml @ 10:77f4c10ef898 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b6b8da66a6eef180ca8e333f98fc4b7575bac7b3
author tomnl
date Thu, 27 Jun 2019 12:42:05 -0400
parents c2806f7ff9b8
children 64a315b27e1c
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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>
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3 Create and SQLite database of an LC-MS(/MS) experiment
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements">
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9 <requirement type="package" >libgfortran</requirement>
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10 </expand>
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11 <stdio>
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12 <exit_code range="1:" />
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13 </stdio>
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14 <command interpreter="Rscript"><![CDATA[
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15 createDatabase.R
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16 --outDir=.
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17 --xset_xa=$xset_xa
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18 --pa=$pa
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19 --xcms_camera_option=$camera_xcms
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20 --cores=\${GALAXY_SLOTS:-4}
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21 #if $file_load_conditional.file_load_select=="yes"
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22 --mzML_files='
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23 #for $i in $file_load_conditional.input
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24 $i,
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25 #end for
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26 '
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27 --galaxy_names='
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28 #for $i in $file_load_conditional.input
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29 $i.name,
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30 #end for
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31 '
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32 #end if
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33
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34 #if $eic
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35 --eic
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36 #end if
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37
0
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38 #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
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39 --grp_peaklist=$grp_peaklist
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40 #end if
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41
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42 ]]></command>
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43 <inputs>
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44 <param type="data" name="xset_xa" label="xcmsSet or CAMERA object"
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45 help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file.
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46 Please specify which to use below"
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47 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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48 <expand macro="camera_xcms" />
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49 <param type="data" name="pa" label="purityA object (frag4feature output)" format="rdata"
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50 help="purityA object saved as 'pa' in a RData file (output from frag4feature)"/>
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51 <param name="eic" type="boolean" label="Include EIC data?"
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52 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
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53 the database. Note, this will take considerable time for large datasets and
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54 the resulting SQLite database can be large"/>
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55 <expand macro="grp_peaklist" />
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56 <expand macro="fileload" />
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57 </inputs>
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58 <outputs>
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59 <data name="createDatabase_output_sqlite" format="sqlite"
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60 label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
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61 from_work_dir="createDatabase_output.sqlite" />
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62
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63 </outputs>
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64 <tests>
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65 <test>
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66 <conditional name="file_load_conditional">
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67 <param name="file_load_select" value="yes"/>
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68 <param name="input" >
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69 <collection type="list">
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70 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
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71 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
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72 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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73 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
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74 </collection>
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75 </param>
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76 </conditional>
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77 <param name="camera_xcms" value="xcms"/>
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78 <param name="xset_xa" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
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79 <param name="pa" value="averageFragSpectra_output_all.RData"/>
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80 <output name="createDatabase_output_sqlite" value="createDatabase_output.sqlite" ftype="sqlite" compare="sim_size"/>
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81 </test>
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82
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83 <test>
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84 <conditional name="file_load_conditional">
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85 <param name="file_load_select" value="yes"/>
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86 <param name="input" >
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87 <collection type="list">
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88 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
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89 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
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90 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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91 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
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92 </collection>
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93 </param>
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94 </conditional>
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95 <param name="camera_xcms" value="xcms"/>
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96 <param name="eic" value="true"/>
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97 <param name="xset_xa" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
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98 <param name="pa" value="averageFragSpectra_output_all.RData"/>
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99 <output name="createDatabase_output_sqlite" value="createDatabase_output_eic.sqlite" ftype="sqlite" compare="sim_size"/>
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100 </test>
0
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101 </tests>
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102
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103 <help><![CDATA[
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104 =============================================================
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105 Create SQLite database for LC-MS(/MS) dataset
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106 =============================================================
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107 ** General **
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108
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109 Create and SQLite database of an LC-MS(/MS) experiment (replaces the create_database function).
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110
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111 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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112
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113 **Example LC-MS/MS processing workflow**
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114
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115 * Purity assessments
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116 + (mzML files) -> purityA -> (pa)
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117 * XCMS processing
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118 + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
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119 * Fragmentation processing
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120 + (xset, pa) -> frag4feature -> filterFragSpectra -> averageAllFragSpectra -> **createDatabase** -> spectralMatching -> (sqlite spectral database)
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121
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122
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123 -----------
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124 Output
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125 -----------
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126 * lcms_sqlite: An SQLite database of the LC-MS(/MS) data (including fragmentation scans)
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127
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128 ]]></help>
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129 <expand macro="citations" />
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130 </tool>