Mercurial > repos > tomnl > assess_purity_msms

annotate assess_purity_msms.xml @ 25:7bff866f72b5 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 25e4ea47403332a6efd413d13a52511eb4ab5110-dirty
author tomnl
date Mon, 11 Jun 2018 07:49:38 -0400
parents faba6cd56875
children 81c4fdfbcb5a
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faba6cd56875 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
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1 <tool id="assess_purity_msms" name="assess_purity_msms" version="0.0.8">
0
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2 <description>
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3 Assess the precursor ion purity for fragmentation spectra acquired from either a LC-MS/MS or DI-MS/MS (MSn) 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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9 <expand macro="requirements" />
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12 <stdio>
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13 <exit_code range="1:" />
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14 </stdio>
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15 <command interpreter="Rscript"><![CDATA[
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16 assess_purity_msms.R
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17 --out_dir=.
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18 #if $mzML_data.format == "mzML_files"
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19 --mzML_files='
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20 #for $i in $mzML_data.source
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21 $i,
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22 #end for
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23 '
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24 --galaxy_names='
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25 #for $i in $mzML_data.source
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26 $i.name,
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27 #end for
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28 '
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29 #elif $mzML_data.format == "library"
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30 --mzML_files $__app__.config.user_library_import_dir/$__user_email__/$mzML_data.source
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31 #end if
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32 #if $offsets.offsets == 'user'
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33 --minOffset=$minoffset
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34 --maxOffset=$maxoffset
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35 #end if
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36
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37 --iwNorm=$iw_norm
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38 --ilim=$ilim
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39
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40 --cores=\${GALAXY_SLOTS:-4}
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41
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42 #if $nearest
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43 --nearest
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44 #end if
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45
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46 #if $mostIntense
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47 --mostIntense
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48 #end if
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49
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50 #if $isotopes.isotopes == "exclude_default"
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51 --exclude_isotopes
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52 #elif $isotopes.isotopes == "user"
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53 --exclude_isotopes
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54 --isotope_matrix=$isotopes.im
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55 #end if
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56
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57 ]]></command>
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58 <inputs>
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59
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60 <conditional name="mzML_data">
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61 <param name="format" type="select" label="Choose the source for the dataset" >
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62 <option value="mzML_files" selected="true">.mzML files to check purity from</option>
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63 <option value="library">Library directory name (to be used with dimspy workflows) or path to
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64 to an individual .mzML file</option>
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65 </param>
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66 <when value="mzML_files">
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67 <param name="source" type="data_collection" format="mzml" label="*.mzML files" >
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68 <validator type="empty_field" />
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69 </param>
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70 </when>
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71 <when value="library">
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72 <param name="source" type="text"
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73 size="40" label="Library directory containing *.mzml files
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74 or path to an individual *.mzML">
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75 <validator type="empty_field" />
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76 </param>
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77 </when>
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78 </conditional>
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79
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80 <param name="mostIntense" type="boolean" checked="true" label="Use most intense peak within isolation window for precursor?"
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81 help="If yes, this will ignore the recorded precursor within the mzML file and use
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82 use the most intense peak within the isolation window to calculate the precursor ion purity"/>
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83
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84 <param name="nearest" type="boolean" checked="true" label="Use nearest full scan to determine precursor?"
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85 help="If yes, this will use the neareset full scan to the fragmentation scan to determine what the m/z value
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86 is of the precursor"/>
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87
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88
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89 <conditional name="offsets">
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90 <param name="offsets" type="select" label="offsets" >
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91 <option value="auto" selected="true">Uses offsets determined in the mzML file</option>
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92 <option value="user">User supplied offset values</option>
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93 </param>
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94 <when value="user">
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95 <expand macro="offsets" />
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96 </when>
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97 <when value="auto">
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98 </when>
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99
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100 </conditional>
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101
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102 <expand macro="general_params" />
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103
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104
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105 </inputs>
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106 <outputs>
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107 <data name="assess_purity_msms" format="tsv" label="${tool.name} on ${on_string}: tsv"
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108 from_work_dir="purity_msms.tsv" />
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109 <data name="assess_purity_msms_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
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110 from_work_dir="purity_msms.RData" />
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111 </outputs>
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112 <tests>
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113 <test>
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114 <conditional name="mzML_data">
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115 <param name="format" value="mzML_files"/>
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116 <param name="source" >
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117 <collection type="list">
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118 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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119 </collection>
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120 </param>
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121 </conditional>
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122 <output name="assess_purity_msms" value="assess_purity_msms_output_LCMSMS1.tsv" />
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123 </test>
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124 </tests>
5
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125
0
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126 <help><![CDATA[
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127 =============================================================
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128 Assess precursor ion purity of MS/MS files
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129 =============================================================
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130 -----------
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131 Description
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132 -----------
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133
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134 Tool to assess precursor ion purity of MS/MS files
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135
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136 Data input of mzML files either from:
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137
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138 * A data collection of the mzML files containing MS/MS scans
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139 * A path to a folder that has mzML files containing MS/MS scans
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140
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141 See Bioconductor documentation for more details about the function used, msPurity::purityA().
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142
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143 -----------
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144 Outputs
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145 -----------
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146
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147 * purity_msms: A tsv file of all the precursor ion purity score (and other metrics) of each fragmentation spectra
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148 * purity_msms_rdata: The purityA object saved as an rdata file
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149
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150
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151 ]]></help>
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152 <expand macro="citations" />
0
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153 </tool>