Mercurial > repos > tomnl > create_sqlite_db

annotate create_sqlite_db.xml @ 19:906e8e2be944 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 04023134d8f28e85927ca293373c506484149ead-dirty
author tomnl
date Thu, 31 May 2018 09:15:28 -0400
parents f13a7d89afdd
children 74917d0e89cc
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1 <tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.15">
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
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40 #if $metfrag_conditional.metfrag_select=="yes"
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41 --metfrag_result=$metfrag_result
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42 #end if
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43
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44 #if $sirius_csifingerid_conditional.sirius_csifingerid_select=="yes"
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45 --sirius_csifingerid_result=$sirius_csifingerid_result
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46 #end if
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47
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48 #if $probmetab_conditional.probmetab_select=="yes"
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49 --probmetab_result=$probmetab_result
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50 #end if
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51
0
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52 #if $eic
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53 --eic
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54 #end if
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55 #if $raw_rt_columns
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56 --raw_rt_columns
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57 #end if
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58 #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
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59 --grp_peaklist=$grp_peaklist
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60 #end if
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61
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62 ]]></command>
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63 <inputs>
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64
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65
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66 <param type="data" name="xset_xa" label="xcmsSet or CAMERA object"
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67 help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file. Please
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68 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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69 <expand macro="camera_xcms" />
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70
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71 <param type="data" name="pa" label="purityA object (frag4feature output)" format="rdata"
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72 help="purityA object saved as 'pa' in a RData file (output from frag4feature)"/>
0
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73
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74 <param name="eic" type="boolean" label="Include EIC data?"
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75 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
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76 the database. Note, this will take considerable time for large datasets and
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77 the resulting SQLite database can be large"/>
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78
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79 <param name="raw_rt_columns" type="boolean" label="Use user defined Raw RT columns?"
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80 help="Only use if the track_rt_raw tool has been used"/>
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81
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82
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83 <expand macro="grp_peaklist" />
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84
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85
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86 <expand macro="fileload" />
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87 <conditional name="metfrag_conditional">
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88 <param name="metfrag_select" type="select" label="Include MetFrag results?">
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89 <option value="no" >no</option>
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90 <option value="yes" >yes</option>
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91 </param>
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92 <when value="no">
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93 </when>
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94 <when value="yes">
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95 <param type="data" name="metfrag_result" label="MetFrag result" format="tsv,tabular"
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96 help="MetFrag result from corresponding dataset"/>
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97 </when>
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98 </conditional>
0
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99
11
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100 <conditional name="sirius_csifingerid_conditional">
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101 <param name="sirius_csifingerid_select" type="select" label="Include Sirius CSI-FingerID results?">
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102 <option value="no" >no</option>
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103 <option value="yes" >yes</option>
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104 </param>
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105 <when value="no">
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106 </when>
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107 <when value="yes">
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108 <param type="data" name="sirius_csifingerid_result" label="Sirius CSI-FingerID result" format="tsv,tabular"
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109 help="Sirius CSI-FingerID result from corresponding dataset"/>
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110 </when>
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111 </conditional>
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112
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113
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114 <conditional name="probmetab_conditional">
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115 <param name="probmetab_select" type="select" label="Include ProbMetab results?">
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116 <option value="no" >no</option>
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117 <option value="yes" >yes</option>
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118 </param>
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119 <when value="no">
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120 </when>
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121 <when value="yes">
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122 <param type="data" name="probmetab_result" label="ProbMetab result" format="tsv,tabular"
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123 help="ProbMetab result from corresponding dataset"/>
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124 </when>
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125 </conditional>
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126
0
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127 </inputs>
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128 <outputs>
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129 <data name="lcms_data_sqlite" format="sqlite" label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db"
4
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130 from_work_dir="lcms_data.sqlite" />
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131 <data name="cpeakgroup_msms" format="tsv" label="${tool.name} on ${on_string}: c-peak-group-msms"
4
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132 from_work_dir="cpeakgroup_msms.tsv" />
0
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133
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134 </outputs>
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135 <tests>
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136 <test>
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137 <conditional name="file_load_conditional">
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138 <param name="file_load_select" value="yes"/>
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139 <param name="input" >
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140 <collection type="list">
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141 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
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142 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
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143 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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144 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
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145 </collection>
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146 </param>
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147 </conditional>
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148 <param name="camera_xcms" value="xcms"/>
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149 <param name="xset_xa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
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150 <param name="pa" value="frag4feature.rdata"/>
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151
0
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152 <output name="cpeakgroup_msms" value="cpeakgroup_msms.tsv" >
13
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153
5
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154
0
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155 </output>
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156 </test>
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157 </tests>
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158
0
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159 <help><![CDATA[
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160 =============================================================
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161 Create SQLite database for LC-MS(/MS) dataset
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162 =============================================================
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163 Create an SQLite database for the msPurity and XCMS (CAMERA) outputs. The SQLite database created can
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164 be used as input to the spectral_matching tool.
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165
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166 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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167
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168 -----------
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169 Output
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170 -----------
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171 * lcms_sqlite: An SQLite database of the LC-MS(/MS) data (including fragmentation scans)
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172 * cpeakgroup_msms: A csv file for all grouped features that have associated fragmentation spectra
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173
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174 ]]></help>
4
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175 <expand macro="citations" />
0
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176 </tool>