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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
author davidecangelosi
date Thu, 02 May 2019 04:49:04 -0400
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1 <?xml version="1.0"?>
2 <tool id="pipe-t" name="PIPE-T" version="1.0" hidden="false">
3 <description>A tool for analyzing RTqPCR expression data </description>
4 <requirements>
5 <requirement type="package" version="3.5.0">r-base</requirement>
6 <requirement type="package" version="7.2.0">libgcc</requirement>
7 <requirement type="package" version="1.36.0">bioconductor-htqpcr</requirement>
8 <requirement type="package" version="3.8.0">bioconductor-rankprod</requirement>
9 <requirement type="package" version="1.56.0">bioconductor-impute</requirement>
10 <requirement type="package" version="1.11.0">r-bbmisc</requirement>
11 <requirement type="package" version="1.8.4">r-psych</requirement>
12 <requirement type="package" version="1.8_1">r-zoo</requirement>
13 <requirement type="package" version="2.10.0">bioconductor-nondetects</requirement>
14 <requirement type="package" version="4.1_1">r-hmisc</requirement>
15 </requirements>
16 <stdio>
17 <exit_code range="1:" />
18 </stdio>
19 <command>
20 <![CDATA[
21 #for $input in $dp.list_files
22 ln -sf '$input' '$__tool_directory__/Symlink/${input.element_identifier}';
23 #end for
24
25 #if str( $dn.condNorm.normMethod ) == "deltaCt":
26 #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "nondetects" or str( $df.condImpute.format ) == "cubic":
27 #if str( $de.condDEA.method ) == "ttest":
28 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
29 #end if
30 #if str( $de.condDEA.method ) == "rp":
31 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
32 #end if
33 #if str( $de.condDEA.method ) == "none":
34 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
35 #end if
36 #end if
37
38 #if str( $df.condImpute.format ) == "knn":
39 #if str( $de.condDEA.method ) == "ttest":
40 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
41 #end if
42 #if str( $de.condDEA.method ) == "rp":
43 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
44 #end if
45 #if str( $de.condDEA.method ) == "none":
46 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
47 #end if
48 #end if
49 #else
50 #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "nondetects" or str( $df.condImpute.format ) == "cubic":
51 #if str( $de.condDEA.method ) == "ttest":
52 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
53 #end if
54 #if str( $de.condDEA.method ) == "rp":
55 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
56 #end if
57 #if str( $de.condDEA.method ) == "none":
58 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
59 #end if
60 #end if
61
62 #if str( $df.condImpute.format ) == "knn":
63 #if str( $de.condDEA.method ) == "ttest":
64 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
65 #end if
66 #if str( $de.condDEA.method ) == "rp":
67 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
68 #end if
69 #if str( $de.condDEA.method ) == "none":
70 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
71 #end if
72 #end if
73 #end if
74 ]]>
75 </command>
76 <inputs>
77 <section name="dp" title="File uploading and parsing" expanded="true">
78 <param name="list_files" type="data_collection" collection_type="list" value="" label="Select a collection list of TaqMan
79 Low Density Array files in the history tab" help="Collection should be of category List. "/>
80 <param name="files" type="data" format="txt" label="Select one of the files in the history tab" help="File should contains only the fields: sampleName and Treatment." />
81 <param name="formatFile" type="select" label="Select one of the file formats from the list below." help="">
82 <option value="EDS" selected="true">EDS</option>
83 <option value="plain">Plain</option>
84 <option value="SDS" >SDS</option>
85 <option value="LightCycler" >LightCycler</option>
86 <option value="CFX">CFX</option>
87 <option value="OpenArray" >OpenArray</option>
88 <option value="BioMark" >BioMark</option>
89 </param>
90 <param name="n" type="integer" min="1" max="1000" value="384" label="Type the number of transcripts in your file" />
91 </section>
92 <section name="dc" title="Ct filtering and categorization" expanded="true">
93 <param name="Ctmin" type="integer" min="0" max="40" value="14" label="Set up a minimum Ct value"
94 help="Any Ct below your selected value will be labelled as Unreliable." />
95 <param name="Ctmax" type="integer" min="0" max="40" value="32" label="Set up a maximum Ct value"
96 help="Any Ct above your selected value will be labelled as Unreliable."/>
97 <param name="flag" type="select" label="Select TRUE if you want that PIPE-T assigns category 'Unreliable' on the basis of FAILURE flag" help="Data in qPCRset objects will have feature categories (Unreliable, Undetermined) assigned to them based on different Ct criteria.">
98 <option value="TRUE">TRUE</option>
99 <option value="FALSE">FALSE</option>
100 </param>
101 </section>
102 <section name="dn" title="Normalization" expanded="true">
103 <conditional name="condNorm">
104 <param name="normMethod" type="select" label="Select one of the normalization methods from the list below." help="Normalization is important to reduce technical variability from the data.">
105 <option value="globalmean" selected="true">Global mean</option>
106 <option value="deltaCt">DeltaCt method (housekeeping genes)</option>
107 <option value="geometric.mean">Modified global mean</option>
108 <option value="quantile">Quantile</option>
109 <option value="norm.rankinvariant">Rank invariant</option>
110 <option value="scale.rankinvariant">Scale rank invariant</option>
111 </param>
112 <when value="deltaCt">
113 <param name="normalizers" type="text" label="Type a comma separated list of housekeeping transcript identifiers that will be used as normalizers." value="U6 snRNA-001973">
114 </param>
115 </when>
116 </conditional>
117 </section>
118 <section name="df" title="Transcript filtering and imputation" expanded="true">
119 <param name="percent" type="integer" min="0" max="100" value="0" label="Set up a percentage of NAs."
120 help="miRs\genes with more than the specified percentage of NAs across samples will be removed." />
121 <param name="filtname" type="text" label="Type a comma separeted list of transcript identifiers to filter out" help="transcript identifiers specified in the List will be removed." value="U6 snRNA-001973,hsa-miR-520a">
122 </param>
123 <conditional name="condImpute">
124 <param name="format" type="select" label="Select one of the imputation methods from the list below." help="">
125 <option value="mestdagh" selected="true">Mestdagh</option>
126 <option value="knn">K-Nearest Neighbour</option>
127 <option value="mean">Mean</option>
128 <option value="median">Median</option>
129 <option value="cubic">Cubic Spline</option>
130 <option value="nondetects">Non-detects</option>
131 </param>
132 <when value="knn">
133 <param name="k" type="integer" min="1" max="100" value="10" label="Type a number of neighbors to use by the KNN imputation method" />
134 <param name="maxp" type="integer" min="1" max="2000" value="1500" label="Type the maximum number of imputed transcript by KNN method." help="Larger numbers are divided by two-means clustering (recursively)
135 prior to imputation. "/>
136 </when>
137 </conditional>
138 </section>
139 <section name="de" title="Differential expression analysis" expanded="true">
140 <conditional name="condDEA">
141 <param name="method" type="select" label="Select one of the methods from the list below or NONE.">
142 <option value="ttest" selected="true">T-test and fold change</option>
143 <option value="rp">Rank Product (Only for unpaired data)</option>
144 <option value="none">NONE</option>
145 </param>
146 <when value="ttest">
147 <param name="alternative" type="select" label="Select one of the types of alternative hypothesis to assess significance.">
148 <option value="two.sided" selected="true">Two sided</option>
149 <option value="greater">Greater</option>
150 <option value="less">Lower</option>
151 </param>
152 <param name="paired" type="select" label="Select TRUE if you want a paired analysis?" help="Pairing of samples will follow the order of the sampleNames in the input file">
153 <option value="TRUE" >TRUE</option>
154 <option value="FALSE" selected="true">FALSE</option>
155 </param>
156 <param name="replicates" type="select" label="Select TRUE if you have replicated miR\gene in your data" help="If replicated miRs\genes are present in the data, the statistics will be calculated once for each replicated miR\gene, rather than the separately.">
157 <option value="TRUE" selected="true">TRUE</option>
158 <option value="FALSE" >FALSE</option>
159 </param>
160 <param name="sort" type="select" label="Select TRUE if you want the output to be sorted by increasing order of p-value?" help="">
161 <option value="TRUE" selected="true">TRUE</option>
162 <option value="FALSE" >FALSE</option>
163 </param>
164 <param name="stringent" type="select" label="Select TRUE to admit more stringent analysis." help=" If stringent is TRUE any unreliable or undetermined measurements among technical and
165 biological replicates will result in the final result being Undetermined. If stringent is FALSE result will be OK unless at least half of the Ct values for a given gene are unreliable/undetermined.">
166 <option value="TRUE" selected="true">TRUE</option>
167 <option value="FALSE" >FALSE</option>
168 </param>
169 <param name="padjust" type="select" label="Select one of the methods to adjust pvalues for multiple hypothesis testing">
170 <option value="BH" selected="true">Benjamini-Hochberg</option>
171 <option value="bonferroni">Bonferroni</option>
172 </param>
173 </when>
174 <when value="rp">
175 </when>
176 </conditional>
177 </section>
178 </inputs>
179 <outputs>
180 <data format="txt" name="galaxy_output1" label="1_Ct_Raw"/>
181 <data format="png" name="galaxy_output2" label="2_Boxplot after data categorization"/>
182 <data format="txt" name="galaxy_output3" label="3_Normalized data"/>
183 <data format="png" name="galaxy_output4" label="4_ECDF"/>
184 <data format="png" name="galaxy_output6" label="5_Boxplot after data normalization"/>
185 <data format="txt" name="galaxy_output5" label="6_Imputed data"/>
186 <data format="txt" name="galaxy_output7" label="7_Differentially Expressed transcripts"/>
187 </outputs>
188
189 <help>
190 <![CDATA[
191 **What it does**
192 INPUTS: This tool parses a list of RTqPCR file and a file with the groups
193 OUTPUTS: and returs
194 1) A txt file with the raw Ct data
195 2) A PNG file with a boxplot of Ct data after data categorization for each sample
196 3) A txt file with deltaCt data after data normalization
197 4) A PNG file with the Empirical cumulative distribution before and after data normalization
198 5) A PNG file with boxplot of deltaCt data after data normalization
199 6) A txt file after imputation of missing values
200 7) A txt file with a number statistics about the significance of each miR\gene
201 ]]>
202 </help>
203 <citations>
204 <citation type="bibtex">
205 @Manual{HTqPCR,
206 title = {HTqPCR: Automated analysis of high-throughput qPCR data.},
207 author = {Heidi Dvinge, Paul Bertone},
208 year = {2009},
209 note = {R package version 1.36.0},
210 url = {http://bioconductor.org/packages/HTqPCR/},
211 }
212 </citation>
213 <citation type="bibtex">
214 @Manual{impute,
215 title = {Impute: Imputation for microarray data.},
216 author = {Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, Gilbert Chu},
217 year = {2018},
218 note = {R package version 1.56.0},
219 url = {http://bioconductor.org/packages/impute/},
220 }
221 </citation>
222 <citation type="bibtex">
223 @Manual{RankProd,
224 title = {RankProd: Rank Product method for identifying differentially expressed
225 genes with application in meta-analysis.},
226 author = {Francesco Del Carratore},
227 year = {2018},
228 note = {R package version 3.8.0},
229 url = {http://bioconductor.org/packages/RankProd/},
230 }
231 </citation>
232 </citations>
233
234 </tool>