Mercurial > repos > tomnl > create_sqlite_db

annotate create_sqlite_db.xml @ 0:fe7d7cc95ca5 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
author tomnl
date Tue, 27 Mar 2018 06:03:50 -0400
parents
children 3a3aab720f52
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1 <tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.1">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5
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6 <expand macro="requirements">
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7 <!-- would ideally have xcms 3.0.0 but not available in bioconda at the point of tool creation-->
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8 </expand>
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9
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10 <description>
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11 Create SQLite database of an XCMS-CAMERA dataset
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12 </description>
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13 <stdio>
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14 <exit_code range="1:" />
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15 </stdio>
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16 <command interpreter="Rscript"><![CDATA[
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17 create_sqlite_db.R
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18 --out_dir=.
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19 --xset_xa=$xset_xa
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20 --pa=$pa
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21 --xcms_camera_option=$camera_xcms
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22 --cores=\${GALAXY_SLOTS:-4}
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23 #if $file_load_conditional.file_load_select=="yes"
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24 --mzML_files='
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25 #for $i in $file_load_conditional.input
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26 $i,
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27 #end for
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28 '
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29 --galaxy_names='
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30 #for $i in $file_load_conditional.input
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31 $i.name,
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32 #end for
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33 '
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34 #end if
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35
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36 #if $eic
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37 --eic
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38 #end if
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39 #if $raw_rt_columns
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40 --raw_rt_columns
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41 #end if
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42 #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
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43 --grp_peaklist=$grp_peaklist
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44 #end if
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45
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46 ]]></command>
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47 <inputs>
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48
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49
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50 <param type="data" name="xset_xa" label="xcmsSet or CAMERA object"
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51 help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file. Please
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52 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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53 <expand macro="camera_xcms" />
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54
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55 <param type="data" name="pa" label="purityA object" format="rdata"
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56 help="purityA object saved as 'pa' in a RData file (output from assess_purity_msms)"/>
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57
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58 <param name="eic" type="boolean" label="Include EIC data?"
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59 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
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60 the database. Note, this will take considerable time for large datasets and
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61 the resulting SQLite database can be large"/>
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62
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63 <param name="raw_rt_columns" type="boolean" label="Use user defined Raw RT columns?"
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64 help="Only use if the track_rt_raw tool has been used"/>
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65
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66
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67 <expand macro="grp_peaklist" />
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68
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69
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70 <expand macro="fileload" />
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71
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72 </inputs>
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73 <outputs>
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74 <data name="lcms_data_sqlite" format="sqlite" label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
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75 from_work_dir="lcms_data.sqlite" visible="true"/>
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76 <data name="cpeakgroup_msms" format="sqlite" label="${tool.name} on ${on_string}: c-peak-group-msms"
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77 from_work_dir="cpeakgroup_msms.tsv" visible="true"/>
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78
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79 </outputs>
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80 <tests>
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81 <test>
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82 <conditional name="file_load_conditional">
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83 <param name="file_load_select" value="yes"/>
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84 <param name="input" >
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85 <collection type="list">
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86 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
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87 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
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88 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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89 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
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90 </collection>
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91 </param>
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92 </conditional>
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93 <param name="camera_xcms" value="xcms"/>
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94 <param name="xset_xa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
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95 <param name="pa" value="frag4feature.rdata"/>
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96 <output name="cpeakgroup_msms" value="cpeakgroup_msms.tsv" >
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97 </output>
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98 </test>
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99 </tests>
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100 <expand macro="citations" />
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101 <help><![CDATA[
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102 =============================================================
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103 Create SQLite database for LC-MS(/MS) dataset
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104 =============================================================
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105 Create an SQLite database for the msPurity and XCMS (CAMERA) outputs. The SQLite database created can
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106 be used as input to the spectral_matching tool.
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107
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108 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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109
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110 -----------
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111 Output
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112 -----------
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113 * lcms_sqlite: An SQLite database of the LC-MS(/MS) data (including fragmentation scans)
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114 * cpeakgroup_msms: A csv file for all grouped features that have associated fragmentation spectra
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115
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116 ]]></help>
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117
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118 </tool>