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annotate frag4feature.xml @ 6:e94ce372d03d draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
author tomnl
date Wed, 04 Apr 2018 16:43:00 -0400
parents 2365c3b350fa
children 9501e9b13b48
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1 <tool id="frag4feature" name="frag4feature" version="0.0.18">
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2 <description>
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3 Assign fragmentation spectra to XCMS features using msPurity
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4 </description>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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10 <expand macro="requirements">
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11 <!-- would ideally have xcms 3.0.0 but not available in bioconda at the point of tool creation-->
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12 <!-- <requirement type="package" version="1.46.0" >bioconductor-xcms</requirement>-->
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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 frag4feature.R
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21 --out_dir=.
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22 --xset=$xset
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23 --pa=$pa
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24 --cores=\${GALAXY_SLOTS:-4}
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25 #if $file_load_conditional.file_load_select=="yes"
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26 --mzML_files='
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27 #for $i in $file_load_conditional.input
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28 $i,
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29 #end for
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30 '
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31 --galaxy_names='
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32 #for $i in $file_load_conditional.input
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33 $i.name,
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34 #end for
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35 '
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36 #end if
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37 --ppm=$ppm_f4f
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38 --plim=$plim_f4f
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39 #if $mostIntense_f4f
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40 --mostIntense
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41 #end if
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42 #if $convert2RawRT_f4f
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43 --convert2RawRT
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44 #end if
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45 #if $createDB
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46 --createDB
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47 #end if
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48
0
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49 #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
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50 --grp_peaklist=$grp_peaklist
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51 #end if
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52
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53 ]]></command>
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54 <inputs>
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55
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56 <param type="data" name="xset" label="xcmsSet object"
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57 help="grouped xcmsSet object saved as 'xset' in an RData file" 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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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="mostIntense_f4f" type="boolean" checked="true" label="For matching fragmentation to a feature,
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62 use most intense peak within isolation window for precursor?"/>
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63
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64 <param name="convert2RawRT_f4f" type="boolean" checked="false" label="Was retention time correction used?"
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65 help="If retention time correction has been used in XCMS set this to yes"/>
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66
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67 <param name="ppm_f4f" type="float" label="ppm" value="10"
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68 help="ppm tolerance between precursor mz and feature mz"/>
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69
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70 <param name="plim_f4f" type="float" label="plim" value="0" max="1" min="0"
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71 help="min purity of precursor to be included"/>
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72
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73 <param name="createDB" type="boolean" checked="true" label="Create SQLite database of spcetra?"/>
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75 <expand macro="grp_peaklist" />
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76
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77 <expand macro="fileload" />
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78
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79 </inputs>
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80 <outputs>
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81 <data name="frag4feature_grouped_msms" format="tsv" label="${tool.name} on ${on_string}: tsv"
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82 from_work_dir="frag4feature.tsv" />
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83 <data name="frag4feature_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
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84 from_work_dir="frag4feature.RData" />
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85 <data name="frag4feature_sqlite" format="sqlite" label="${tool.name} on ${on_string}: Sqlite"
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86 from_work_dir="alldata.sqlite" />
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87 </outputs>
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88 <tests>
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89 <test>
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90 <conditional name="file_load_conditional">
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91 <param name="file_load_select" value="yes"/>
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92 <param name="input" >
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93 <collection type="list">
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94 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
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95 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
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96 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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97 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
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98 </collection>
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99 </param>
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100 </conditional>
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101 <param name="xset" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
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102 <param name="pa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.assess_purity.rdata"/>
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103 <output name="frag4feature_grouped_msms" value="frag4feature_output.tsv" >
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104 </output>
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105 </test>
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106 </tests>
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107
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108 <help><![CDATA[
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109 =============================================================
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110 Link fragmentation spectra to XCMS features
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111 =============================================================
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112 -----------
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113 Description
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114 -----------
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115
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116 Tool to link XCMS features to fragmentation spectra and create an SQLite database of all the data and connections.
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117
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118 Please note that the xcmsSet object needs to have been grouped.
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119
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120 The data inputs are:
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121
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122 * A purityA object (generated from assess_purity_msms) saved in an rdata file.
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123 * A xcmsSet grouped object (generated from xcms_group) saved in an rdata file
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124 * [optional] a dataset collection of the mzML files to resubmit
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125
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126 See Bioconductor documentation for more details, function msPurity::frag4feature()
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127
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128 -----------
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129 Outputs
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130 -----------
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131 * frag4feature_rdata: An updated purityA object saved as rdata file with fragmentation-feature links added
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132 * frag4feature_grouped_msms: A flat file of all the XCMS peaks for each grouped feature and the corresponding fragmentation scans
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133 * frag4feature_sqlite: An SQLite database of the data (including fragmentation scans)
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134
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135
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136
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137 ]]></help>
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138
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139 <expand macro="citations" />
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140
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141 </tool>