Mercurial > repos > tomnl > deconrank

annotate deconrank.xml @ 14:5b0eceae2d6c draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 2864a500a25e87f292f185872b92ecfe5800dea1
author tomnl
date Fri, 04 May 2018 12:49:30 -0400
parents d3a5012ef348
children e32ab9b71b79
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14
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1 <tool id="deconrank" name="deconrank" version="0.3.12">
0
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2 <description>Deconvolute adducts and isotopes then score and rank for fragmentation</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.6">deconrank</requirement>
0
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9
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10 <command ><![CDATA[
1
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11 echo "$irm" &&
0
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12 python -m deconrank
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13 -i $peaks_file
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14 -o .
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15 --delim tab
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16 #if not $polarity == "auto"
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17 --pol $polarity
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18 #end if
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19 --tech $technology
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20 --pol $polarity
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21 #if $rulescores == "user"
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22 --rp $rulescores.rulescores
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23 #end if
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24 --pthr $pthr
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25 --stp $stp
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26 --irm "$irm"
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27 --max_time $dschedule.max_time
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28 --min_time $dschedule.min_time
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29 --max_cid_time $dschedule.max_cid_time
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30 --peak_time_cid $dschedule.peak_time_cid
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31 --peak_time_hcd $dschedule.peak_time_hcd
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32 --percentage_cid $dschedule.percentage_cid
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33 --delay_time $dschedule.delay_time
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34 #if $full_output
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35 --full_output
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36 #end if
1
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37 #if $dschedule.template_cond.template_select == "user"
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38 --method_template_name '$dschedule.template_cond.template_name'
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39 #end if
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40 --target_name '$peaks_file.element_identifier'
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41
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42 && ls && pwd
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43
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44 ]]></command>
0
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45
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46 <inputs>
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47 <param type="data" name="peaks_file" format="tabular,tsv"
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48 help="tsv or tabular file with mz and intensity columns"/>
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49
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50 <param name="technology" type="select" label="technology" help="Mass spectrometry technology used" >
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51 <option value="lcms" selected="true">LC-MS</option>
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52 <option value="dims">DI-MS</option>
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53 </param>
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54
1
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55 <param name="polarity" type="select" label="polarity" help="polarity [pos, neg]" >
0
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56 <option value="pos" >positive</option>
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57 <option value="neg">negative</option>
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58 </param>
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59
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60 <conditional name="rulescores">
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61 <param name="rulescores" type="select" label="Scores for adducts" >
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62 <option value="default" >Default</option>
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63 <option value="user" >Provide a csv file of the rules to use</option>
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64 </param>
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65 <when value="user">
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66 <param type="data" name="rulescores" format="tsv, tabular"
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67 help="User supplied rules file used to for scoring adducts, should contain at least
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68 2 columns: [name, fragscore]
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69 Where a score of 1 indicates the adduct is the best adduct form to fragment"/>
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70 </when>
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71 <when value="default"> </when>
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72 </conditional>
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73
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74 <param name="pthr" label="precursor ion purity threshold" type="float" value="0.4" min="0" max="1"/>
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75 <param name="stp" label="Second tier percentage" type="float" value="0.0" min="0" max="1"
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76 help="Second tier percentage, % of second tier that we go into the target list. should be in decimal
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77 format i.e. 0.1 = 10%. Default is to remove all second tier peaks (i.e. set to 0.0)"/>
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78
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79 <param name="irm" type="select" multiple="true" label="isotope removal" help="" >
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80 <option value="[M]+">[M]+</option>
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81 <option value="[M+1]+" selected="true">[M+1]+</option>
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82 <option value="[M+2]+" selected="true" >[M+2]+</option>
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83 <option value="[M+3]+">[M+3]+</option>
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84 <option value="[M+4]+">[M+4]+</option>
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85 <option value="[M]2+">[M]2+</option>
3
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86 <option value="[M+1]2+" selected="true">[M+1]2+</option>
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87 <option value="[M+2]2+" selected="true">[M+2]2+</option>
0
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88 <option value="[M+3]2+">[M+3]2+</option>
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89 <option value="[M+4]2+">[M+4]2+</option>
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90 <option value="[M]3+">[M]3+</option>
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91 <option value="[M+1]3+">[M+1]3+</option>
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92 <option value="[M+2]3+">[M+2]3+</option>
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93 <option value="[M+3]3+">[M+3]3+</option>
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94 <option value="[M+4]3+">[M+4]3+</option>
3
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95
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96 <option value="[M]-">[M]-</option>
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97 <option value="[M+1]-" selected="true">[M+1]-</option>
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98 <option value="[M+2]-" selected="true" >[M+2]-</option>
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99 <option value="[M+3]-">[M+3]-</option>
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100 <option value="[M+4]-">[M+4]-</option>
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101 <option value="[M]2-">[M]2-</option>
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102 <option value="[M+1]2-" selected="true" >[M+1]2-</option>
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103 <option value="[M+2]2-" selected="true" >[M+2]2-</option>
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104 <option value="[M+3]2-" >[M+3]2-</option>
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105 <option value="[M+4]2-">[M+4]2-</option>
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106 <option value="[M]3-">[M]3-</option>
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107 <option value="[M+1]3-">[M+1]3-</option>
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108 <option value="[M+2]3-">[M+2]3-</option>
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109 <option value="[M+3]3-">[M+3]3-</option>
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110 <option value="[M+4]3-">[M+4]3-</option>
0
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111 </param>
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112
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113 <param name="full_output" type="boolean" label="Use extended output for the scores tsv file?"/>
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114
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115 <section name="weights" title="Weightings for scores" expanded="False" help="All values need to sum to 1">
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116 <param name="adduct" type="float" value="0.3" min="0" max="1"/>
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117 <param name="intensity" type="float" value="0.3" min="0" max="1" />
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118 <param name="precursor-ion-purity" type="float" value="0.2" min="0" max="1" />
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119 <param name="clustern" type="float" value="0.2" min="0" max="1" />
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120 </section>
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121
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122
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123
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124
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125 <section name="dschedule" title="Scheduling features for DIMS fragmentation experimental run" expanded="False">
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126 <param name="max_time" type="float" value="1800" help="Max time for run (secs)"/>
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127 <param name="min_time" type="float" value="120" help="Min time for run (secs)"/>
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128 <param name="max_cid_time" type="float" value="300" help="Max time to perform CID fragmentation (secs)" />
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129 <param name="peak_time_hcd" type="float" value="10" help="Time to fragment a peak using HCD (secs)" />
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130 <param name="peak_time_cid" type="float" value="12" help="Time to fragment a peak using CID (secs)" />
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131 <param name="percentage_cid" type="float" value="0.333" min="0" max="1" help="Percentage of time fragmenting using
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132 CID (rather than HCD)"/>
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133 <param name="delay_time" type="float" value="24" help="Delay time before acquisition begins (secs)"/>
1
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134
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135 <conditional name="template_cond">
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136 <param name="template_select" type="select" label="Use default method template file names?"
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137 help="Default names are: Neg_MSMS_MSn.meth and Pos_MSMS_MSn.meth">
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138 <option value="default" >Default</option>
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139 <option value="user" >Provide name</option>
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140 </param>
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141 <when value="user">
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142 <param name="template_name" label="method template name" type="text" />
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143 </when>
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144 <when value="default"> </when>
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145 </conditional>
0
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146 </section>
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147
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148
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149 </inputs>
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150 <outputs>
1
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151 <data name="scores" label="${tool.name} on ${on_string}: scores"
0
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152 from_work_dir="scores.tsv" format="tsv"/>
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153 <data name="traceback" label="${tool.name} on ${on_string}: traceback"
0
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154 from_work_dir="traceback.tsv" format="tsv"/>
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155
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156 <collection name="targets" type="list" label="${tool.name} on ${on_string}: targets" format="tsv">
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157 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" directory="targets" format="tsv" visible="false"
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158 assign_primary_output="true"/>
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159 <filter>technology == "dims"</filter>
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160 </collection>
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161
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162 <data name="XcaliburAutoInput" label="${tool.name} on ${on_string}: XcaliburAutoInput"
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163 from_work_dir="xcalibur_auto_input.tsv" format="tsv">
0
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164 <filter>technology == "dims"</filter>
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165 </data>
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166
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167 </outputs>
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168 <tests>
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169 <test>
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170 <param name="peaks_file" value="camera_annotated_peaklist.txt" ftype="tsv"/>
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171 <param name="technology" value="dims"/>
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172 <param name="polarity" value="pos"/>
1
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173 <output name="scores" value="scores.tsv"/>
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174 <output name="traceback" value="traceback.tsv"/>
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175 <output name="XcaliburAutoInput" value="XcaliburAutoInput.tsv"/>
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176 <output name="target" value="target.tsv"/>
0
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177 </test>
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178 </tests>
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179
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180 <help><![CDATA[
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181 Deconvolute adducts and isotopes then score and rank for fragmentation
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182
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183 ]]></help>
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184 <citations> </citations>
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185 </tool>