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comparison askor_de.xml @ 0:ceef9bc6bbc7 draft

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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/askor commit 08a187f91ba050d584e586d2fcc99d984dac607c
author genouest
date Thu, 12 Apr 2018 05:23:45 -0400
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children 6bbc90a11c3f
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-1:000000000000 0:ceef9bc6bbc7
1 <tool id="askor_de" name="AskoR DE" version="0.1">
2 <description>EdgeR for AskOmics</description>
3 <requirements>
4 <requirement type="package" version="3.34.6">bioconductor-limma</requirement>
5 <requirement type="package" version="1.4.30">r-statmod</requirement>
6 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
7 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
8 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
9 <requirement type="package" version="0.7.0">r-ggrepel</requirement>
10 <requirement type="package" version="3.0.1">r-gplots</requirement>
11 <requirement type="package" version="1.4.4">r-optparse</requirement>
12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[
14 export ASKOR_PATH='$__tool_directory__'
15
16 &&
17
18 Rscript '$__tool_directory__/AskoR_DE.R'
19 --out '${out_pdf}'
20 --outdir askor_output
21 --fileofcount '${fileofcounts}'
22 --sample '${samples}'
23 --contrasts '${contrasts}'
24 #if $adv.organism
25 --org '${adv.organism}'
26 #end if
27 #if $adv.colgenes
28 --col_genes ${adv.colgenes}
29 #end if
30 #if $adv.palette
31 --palette '${adv.palette}'
32 #end if
33 #if $selection.sel
34 --select '${selection.sel}'
35 #end if
36 #if $selection.remove
37 --remove '${selection.remove}'
38 #end if
39 #if $thresholds.th_cpm
40 --th_cpm ${thresholds.th_cpm}
41 #end if
42 #if $thresholds.rep
43 --rep ${thresholds.rep}
44 #end if
45 #if $thresholds.th_FDR
46 --th_FDR ${thresholds.th_FDR}
47 #end if
48 #if $stats.norm
49 --normalization '${stats.norm}'
50 #end if
51 #if $stats.adj
52 --adj '${stats.adj}'
53 #end if
54 #if $stats.glm
55 --glm '${stats.glm}'
56 #end if
57 #if $adv.nh
58 --nh ${adv.nh}
59 #end if
60 ]]></command>
61 <inputs>
62 <param format="csv" name="fileofcounts" type="data" label="File of counts" />
63 <param format="tsv" name="samples" type="data" label="Descriptions of the samples" />
64 <param format="tsv" name="contrasts" type="data" label="Descriptions of the contrasts" />
65 <section name="adv" title="Format options" expanded="false">
66 <param name="colgenes" type="integer" label="Column of the genes" value="1" optional="true" />
67 <!--param name="sep" type="text" label="Field separator" value="\t" optional="true" /-->
68 <param name="palette" type="text" label="Color palette (Rcolorbrewer)" value="Set2" optional="true" />
69 <param name="organism" type="text" label="Organism" value="Asko" optional="true" />
70 <param name="nh" type="integer" label="Number of genes in the heatmap" value="50" optional="true" />
71 </section>
72 <section name="selection" title="Samples selection options" expanded="false">
73 <param name="sel" type="text" label="List of selected samples (separated by comma)" optional="true" />
74 <param name="remove" type="text" label="List of removed samples (separated by comma)" optional="true" />
75 </section>
76 <section name="thresholds" title="Threshold options" expanded="false">
77 <param name="th_cpm" type="float" label="Minimum CPM value for selecting a gene" value="0.5" optional="true" />
78 <param name="rep" type="integer" label="Number of samples with CPM > th_comp for selecting a gene" value="3" optional="true" />
79 <param name="th_FDR" type="float" label="FDR threshold for reporting a differential gene" value="0.05" optional="true" />
80 </section>
81 <section name="stats" title="Statistics options" expanded="false">
82 <param name="norm" type="select" label="Normalization method">
83 <option value="TMM">TMM</option>
84 <option value="RLE">RLE</option>
85 <option value="upperquartile">Upperquartile</option>
86 <option value="none">None</option>
87 </param>
88 <param name="glm" type="select" label="GLM method">
89 <option value="qlf">qlf</option>
90 <option value="lrt">lrt</option>
91 </param>
92 <param name="adj" type="select" label="Multitest correction method">
93 <option value="fdr">fdr</option>
94 <option value="holm">holm</option>
95 <option value="hochberg">hochberg</option>
96 <option value="hommel">hommel</option>
97 <option value="bonferroni">bonferroni</option>
98 <option value="BH">BH</option>
99 <option value="BY">BY</option>
100 <option value="none">none</option>
101 </param>
102 </section>
103 </inputs>
104 <outputs>
105 <data format="pdf" name="out_pdf" label="${tool.name} on ${on_string}: Graphics" />
106 <data name="output" format="tsv" label="${tool.name} on ${on_string}">
107 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" ext="tsv" visible="true" directory="askor_output" />
108 </data>
109 </outputs>
110 <tests>
111 <test>
112 <param name="fileofcounts" ftype="csv" value="counts.csv" />
113 <param name="samples" ftype="tsv" value="Samples.txt" />
114 <param name="contrasts" ftype="tsv" value="Contrasts.txt" />
115 <section name="adv">
116 <param name="colgenes" value="3" />
117 </section>
118 <section name="thresholds">
119 <param name="th_cpm" value="10" />
120 </section>
121 <output name="out_pdf" file="out.pdf" compare="sim_size"/>
122 <output name="output">
123 <discovered_dataset designation="AskoAvsK" ftype="tsv" file="AskoAvsK.txt" compare="sim_size" />
124 <discovered_dataset designation="AskoT1AvsT1K" ftype="tsv" file="AskoT1AvsT1K.txt" compare="sim_size" />
125 <discovered_dataset designation="AskoT1vsT0" ftype="tsv" file="AskoT1vsT0.txt" compare="sim_size" />
126 <discovered_dataset designation="AskoT1vsT2" ftype="tsv" file="AskoT1vsT2.txt" compare="sim_size" />
127 <discovered_dataset designation="condition.asko" ftype="tsv" file="condition.asko.txt" compare="sim_size" />
128 <discovered_dataset designation="context.asko" ftype="tsv" file="context.asko.txt" compare="sim_size" />
129 <discovered_dataset designation="contrast.asko" ftype="tsv" file="contrast.asko.txt" compare="sim_size" />
130 </output>
131 </test>
132 </tests>
133 <help><![CDATA[
134 This tools generates a list of differential genes from various contrasts in an AskOmics format (https://askomics.github.io/).
135
136 Example tabular input file of counts:
137
138 ============ ========== =============== =========== =========== ======
139 miRNA read_count precursor total A32 A34
140 ------------ ---------- --------------- ----------- ----------- ------
141 GL349623_679 346.00 GL349623_679 146.00 16.00 130.0
142 GL349624_956 13.00 GL349624_956 13.00 0 13.0
143 ============ ========== =============== =========== =========== ======
144
145 Example tabular sample description file:
146
147 ============ ========== =============== ===========
148 ID condition stage treatment
149 ------------ ---------- --------------- -----------
150 A32 T3A T3 Acetone
151 A34 T3A T3 Acetone
152 ============ ========== =============== ===========
153
154 Example tabular contrast description file:
155
156 ============ ========================= =======================
157 Contrast context1_of@Context context2_of@Context
158 ------------ ------------------------- -----------------------
159 T1vsT0 T1 T0
160 T1vsT2 T1 T2
161 ============ ========================= =======================
162 ]]></help>
163 <citations>
164 </citations>
165 </tool>