Mercurial > repos > tomnl > lcms_interval_scheduling

annotate lcms-interval-scheduling.xml @ 4:fe2d05d5731a draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 578fd07833b93847193666c11744ba0bca1aaf57-dirty
author tomnl
date Thu, 03 May 2018 06:59:38 -0400
parents 21a76537a900
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1 <tool id="lcms_interval_scheduling" name="lcms_interval_scheduling" version="0.0.2">
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2 <requirements>
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3 <requirement type="package" >r</requirement>
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4 <requirement type="package" >r-optparse</requirement>
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5 <requirement type="package" >r-xcmswrapper</requirement>
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6 </requirements>
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7 <description>Generate target lists from LC-MS features for a fragmentation experiment
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8 </description>
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9
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10 <stdio>
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11 <exit_code range="1:" />
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12 </stdio>
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13 <command interpreter="Rscript"><![CDATA[
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14 lcms-interval-scheduling.R
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15
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16 --sample_peaklist=$sample_peaklist
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17 --blank_peaklist=$blank_peaklist
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18 --topn=$topn
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19 --out_dir=.
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20 --method=$method_select.method
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21 #if $method_select.method=='metshot'
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22 #if $method_select.fillgaps
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23 --fillgaps
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24 #end if
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25 #elif $method_select.method=='simple'
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26 --maxms2=$method_select.maxms2
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27 --ilimit=$method_select.ilimit
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28 #else
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29 --overlappingP=$method_select.overlappingP
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30 #end if
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31 --widthFactor=$widthFactor
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32 --minWidth=$minWidth
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33 --shift=$shift
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34 --samplelistNm=$samplelistNm
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35 #if $fullpw
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36 --fullpw
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37 #end if
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38 --b_widthFactor=$b_widthFactor
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39 --b_shift=$b_shift
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40 --b_exclu_limit=$b_exclu_limit
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41 --b_minWidth=$b_minWidth
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42 --polarity=$polarity
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43 #if $dma_nearline_cond.dma=='yes'
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44 --blankClass=$dma_nearline_cond.blankClass
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45 --filterS=$dma_nearline_cond.filterS
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46 --dmaNearline
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47 #end if
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48 --intensityCN=$intensityCN
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49 --sortCN=$sortCN
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50 ]]></command>
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51 <inputs>
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52 <param type="data" name="sample_peaklist" label="Sample peaklist" format="tsv,tabular"
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53 help="The peaklist from the samples to be scheduled for fragmentation"/>
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54
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55 <param type="data" name="blank_peaklist" label="Blank peaklist" format="tsv,tabular"
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56 help="The peaklist of blank features to avoid when performing fragmentation"/>
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57
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58 <param type="data" name="topn" label="Topn blank peaklist" format="tsv,tabular"
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59 help="The top (n) blank peaks determined from windows of the spectrum (i.e. not using XCMS)"/>
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60
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61 <conditional name="method_select">
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62 <param name="method" type="select" label="Nearline method">
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63 <option value="simple" >Simple nearline (divide equally amongst runs) </option>
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64 <option value="interval">Interval schedule with defined overlap</option>
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65 <option value="interval_min_overlap" selected="true">Interval schedule with defined overlap. Overlap is also minimized</option>
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66 <option value="metshot">Original metshot algorithm (No overlapping features)</option>
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67 </param>
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68 <when value="metshot">
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69 <param name="fillGaps" type="boolean" label="Fill gaps"/>
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70 </when>
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71 <when value="simple">
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72 <param name="maxms2" type="integer" label="Max MS2 per run" value="2000"/>
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73 <param name="ilimit" type="float" label="Intensity (peak area) limit to be included" value="5000"/>
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74 </when>
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75 <when value="interval">
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76 <param name="overlappingP" type="integer" label="Max number of overlapping peaks" value="10"/>
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77 </when>
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78 <when value="interval_min_overlap">
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79 <param name="overlappingP" type="integer" label="Max number of overlapping peaks" value="10"/>
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80 </when>
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81 </conditional>
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82
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83 <param name="widthFactor" type="float" label="Width factor" value="1"
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84 help="Increase the width of the peaks by the chosen factor "/>
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85
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86 <param name="minWidth" type="float" label="Minimum width of peak (sec)" value="5"
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87 help="The time range will always be >= to this value (even if the prior peak width is calculated
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88 to be smaller)"/>
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89
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90 <param name="shift" type="float" label="Shift (sec)" value="0" help="Shift all the peaks by value to account for drift"/>
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91 <param name="samplelistNm" type="integer" label="Number of MS2 runs to perform" value="4"/>
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92 <param name="fullpw" type="boolean" label="Use full peak width?" help="" />
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93 <param name="b_widthFactor" type="float" label="Width factor (for blank)" value="2"
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94 help="Increase the width of the peaks by the chosen factor "/>
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95
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96 <param name="b_minWidth" type="float" label="Minimum width of peak (sec) (for blank)" value="5"
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97 help="The time range will always be >= to this value (even if the prior peak width is calculated
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98 to be smaller) (for blank)"/>
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99
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100
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101 <param name="b_shift" type="float" label="Shift (for blank) (sec)" value="0" help="Shift all the peaks by value to account for drift"/>
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102 <param name="b_exclu_limit" type="integer" label="Exclusion limit" value="5000" help="Limit of peaks to put on exclusion limit"/>
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103 <param name="polarity" type="select" label="Polarity">
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104 <option value="positive" selected="true" >Positive</option>
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105 <option value="negative" >Negative</option>
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106 </param>
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107
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108 <param name="sortCN" type="text" label="column of sample peaklist to order by" value="totalS"
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109 help="default value corresponds if the tool 'deconrank' has been run prior. The 'total score'
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110 column is based on multiple criteria (see deconrank tool).
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111 If not using the deconrank tool, any other column can be used e.g. intensity (peak area)"/>
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112
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113 <param name="intensityCN" type="text" label="column to use for intensity (peak area) for sample" value="i"/>
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114
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115
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116 <conditional name="dma_nearline_cond">
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117 <param name="dma" type="select" label="Use as part of DMA nearline workflow?"
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118 help="If using within the nearline LC-MS workflow then certain processing needs to be performed,
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119 including filtering out peaks that are not to be scheduled">
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120 <option value="yes">Yes</option>
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121 <option value="no" select="no">No</option>
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122 </param>
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123 <when value="yes">
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124 <param name="blankClass" type="text" label="Blank class" value="blank"
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125 help="Note that this will have to change if the blank class has a different name. Uses the valid
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126 column e.g. [blank_name]_valid.
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127 If he value is 1 (we keep) if 0 (we do not use)" />
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128 <param name="filterS" type="text" label="Column name to filter sample on" value="excludedFinal"
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129 help="This is a bit confusing.. But if this value is 1 then (we exclude) and if 0 (we keep for the
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130 sample)"/>
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131 </when>
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132 </conditional>
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133
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134 </inputs>
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135 <outputs>
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136 <collection name="inclusion_lists" type="list" label="${tool.name} on ${on_string}: inclusion lists">
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137 <discover_datasets pattern="(?P&lt;designation&gt;.+inclusion.+).csv" format="csv" directory="." />
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138 </collection>
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139 <collection name="exclusion_lists" type="list" label="${tool.name} on ${on_string}: exclusion lists">
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140 <discover_datasets pattern="(?P&lt;designation&gt;.+exclusion.+).csv" format="csv" directory="." />
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141 </collection>
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142 <data format="pdf" name="overlap_plots_positive" label="${tool.name} on ${on_string}: overlap plots"
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143 from_work_dir="overlap_plots_positive.pdf"/>
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144
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145 </outputs>
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146 <tests>
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147 </tests>
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148 <help><![CDATA[
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149
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150 ]]></help>
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151 </tool>