Mercurial > repos > genouest > askor_de

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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/askor commit 994ecff7807bb0eb9dac740d67ad822415b0b464
author genouest
date Thu, 19 Apr 2018 03:44:31 -0400
parents 6bbc90a11c3f
children
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6bbc90a11c3f planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/askor commit dea4b3dfc2393e4f5b9945099cfec37afe471283
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1 <tool id="askor_de" name="AskoR DE" version="0.2">
0
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2 <description>EdgeR for AskOmics</description>
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3 <requirements>
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4 <requirement type="package" version="3.34.6">bioconductor-limma</requirement>
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5 <requirement type="package" version="1.4.30">r-statmod</requirement>
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6 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
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7 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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8 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
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9 <requirement type="package" version="0.7.0">r-ggrepel</requirement>
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10 <requirement type="package" version="3.0.1">r-gplots</requirement>
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11 <requirement type="package" version="1.4.4">r-optparse</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
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14 export ASKOR_PATH='$__tool_directory__'
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15
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16 &&
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17
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18 Rscript '$__tool_directory__/AskoR_DE.R'
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19 --out '${out_pdf}'
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20 --outdir askor_output
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21 --fileofcount '${fileofcounts}'
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22 --sample '${samples}'
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23 --contrasts '${contrasts}'
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24 #if $adv.organism
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25 --org '${adv.organism}'
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26 #end if
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27 #if $adv.colgenes
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28 --col_genes ${adv.colgenes}
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29 #end if
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30 #if $adv.palette
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31 --palette '${adv.palette}'
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32 #end if
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33 #if $selection.sel
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34 --select '${selection.sel}'
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35 #end if
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36 #if $selection.remove
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37 --remove '${selection.remove}'
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38 #end if
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39 #if $thresholds.th_cpm
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40 --th_cpm ${thresholds.th_cpm}
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41 #end if
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42 #if $thresholds.rep
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43 --rep ${thresholds.rep}
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44 #end if
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45 #if $thresholds.th_FDR
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46 --th_FDR ${thresholds.th_FDR}
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47 #end if
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48 #if $stats.norm
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49 --normalization '${stats.norm}'
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50 #end if
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51 #if $stats.adj
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52 --adj '${stats.adj}'
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53 #end if
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54 #if $stats.glm
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55 --glm '${stats.glm}'
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56 #end if
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57 #if $adv.nh
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58 --nh ${adv.nh}
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59 #end if
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60 ]]></command>
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61 <inputs>
2
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62 <param format="tabular,tsv,csv" name="fileofcounts" type="data" label="File of counts" />
1
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63 <param format="tabular,tsv" name="samples" type="data" label="Descriptions of the samples" />
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64 <param format="tabular,tsv" name="contrasts" type="data" label="Descriptions of the contrasts" />
0
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65 <section name="adv" title="Format options" expanded="false">
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66 <param name="colgenes" type="integer" label="Column of the genes" value="1" optional="true" />
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67 <!--param name="sep" type="text" label="Field separator" value="\t" optional="true" /-->
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68 <param name="palette" type="text" label="Color palette (Rcolorbrewer)" value="Set2" optional="true" />
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69 <param name="organism" type="text" label="Organism" value="Asko" optional="true" />
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70 <param name="nh" type="integer" label="Number of genes in the heatmap" value="50" optional="true" />
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71 </section>
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72 <section name="selection" title="Samples selection options" expanded="false">
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73 <param name="sel" type="text" label="List of selected samples (separated by comma)" optional="true" />
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74 <param name="remove" type="text" label="List of removed samples (separated by comma)" optional="true" />
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75 </section>
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76 <section name="thresholds" title="Threshold options" expanded="false">
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77 <param name="th_cpm" type="float" label="Minimum CPM value for selecting a gene" value="0.5" optional="true" />
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78 <param name="rep" type="integer" label="Number of samples with CPM > th_comp for selecting a gene" value="3" optional="true" />
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79 <param name="th_FDR" type="float" label="FDR threshold for reporting a differential gene" value="0.05" optional="true" />
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80 </section>
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81 <section name="stats" title="Statistics options" expanded="false">
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82 <param name="norm" type="select" label="Normalization method">
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83 <option value="TMM">TMM</option>
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84 <option value="RLE">RLE</option>
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85 <option value="upperquartile">Upperquartile</option>
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86 <option value="none">None</option>
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87 </param>
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88 <param name="glm" type="select" label="GLM method">
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89 <option value="qlf">qlf</option>
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90 <option value="lrt">lrt</option>
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91 </param>
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92 <param name="adj" type="select" label="Multitest correction method">
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93 <option value="fdr">fdr</option>
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94 <option value="holm">holm</option>
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95 <option value="hochberg">hochberg</option>
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96 <option value="hommel">hommel</option>
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97 <option value="bonferroni">bonferroni</option>
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98 <option value="BH">BH</option>
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99 <option value="BY">BY</option>
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100 <option value="none">none</option>
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101 </param>
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102 </section>
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103 </inputs>
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104 <outputs>
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105 <data format="pdf" name="out_pdf" label="${tool.name} on ${on_string}: Graphics" />
1
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106 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
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107 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" ext="tabular" visible="true" directory="askor_output" />
0
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108 </data>
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109 </outputs>
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110 <tests>
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111 <test>
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112 <param name="fileofcounts" ftype="csv" value="counts.csv" />
1
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113 <param name="samples" ftype="tabular" value="Samples.txt" />
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114 <param name="contrasts" ftype="tabular" value="Contrasts.txt" />
0
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115 <section name="adv">
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116 <param name="colgenes" value="3" />
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117 </section>
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118 <section name="thresholds">
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119 <param name="th_cpm" value="10" />
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120 </section>
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121 <output name="out_pdf" file="out.pdf" compare="sim_size"/>
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122 <output name="output">
1
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123 <discovered_dataset designation="AskoAvsK" ftype="tabular" file="AskoAvsK.txt" compare="sim_size" />
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124 <discovered_dataset designation="AskoT1AvsT1K" ftype="tabular" file="AskoT1AvsT1K.txt" compare="sim_size" />
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125 <discovered_dataset designation="AskoT1vsT0" ftype="tabular" file="AskoT1vsT0.txt" compare="sim_size" />
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126 <discovered_dataset designation="AskoT1vsT2" ftype="tabular" file="AskoT1vsT2.txt" compare="sim_size" />
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127 <discovered_dataset designation="condition.asko" ftype="tabular" file="condition.asko.txt" compare="sim_size" />
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128 <discovered_dataset designation="context.asko" ftype="tabular" file="context.asko.txt" compare="sim_size" />
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129 <discovered_dataset designation="contrast.asko" ftype="tabular" file="contrast.asko.txt" compare="sim_size" />
0
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130 </output>
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131 </test>
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132 </tests>
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133 <help><![CDATA[
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134 This tools generates a list of differential genes from various contrasts in an AskOmics format (https://askomics.github.io/).
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135
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136 Example tabular input file of counts:
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137
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138 ============ ========== =============== =========== =========== ======
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139 miRNA read_count precursor total A32 A34
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140 ------------ ---------- --------------- ----------- ----------- ------
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141 GL349623_679 346.00 GL349623_679 146.00 16.00 130.0
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142 GL349624_956 13.00 GL349624_956 13.00 0 13.0
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143 ============ ========== =============== =========== =========== ======
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144
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145 Example tabular sample description file:
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146
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147 ============ ========== =============== ===========
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148 ID condition stage treatment
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149 ------------ ---------- --------------- -----------
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150 A32 T3A T3 Acetone
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151 A34 T3A T3 Acetone
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152 ============ ========== =============== ===========
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153
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154 Example tabular contrast description file:
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155
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156 ============ ========================= =======================
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157 Contrast context1_of@Context context2_of@Context
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158 ------------ ------------------------- -----------------------
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159 T1vsT0 T1 T0
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160 T1vsT2 T1 T2
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161 ============ ========================= =======================
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162 ]]></help>
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163 <citations>
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164 </citations>
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165 </tool>