annotate cpm_tpm_rpk.xml @ 3:8b1020c25f0f draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
author artbio
date Fri, 12 Apr 2019 12:01:35 -0400
parents 563337e780ce
children be358a1ebf67
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
1 <tool id="cpm_tpm_rpk" name="Generate CPM, TPM, RPK" version="0.4.0">
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
2 <description>from raw counts expression values</description>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
3 <requirements>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
4 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
5 <requirement type="package" version="0.13=r3.3.2_0">r-rtsne</requirement>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
6 <requirement type="package" version="2.2.1=r3.3.2_0">r-ggplot2</requirement>
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
7 <requirement type="package" version="0.4.1=r3.3.2_0">r-ggfortify</requirement>
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
8 </requirements>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
9 <stdio>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
10 <exit_code range="1:" level="fatal" description="Tool exception" />
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
11 </stdio>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
13 Rscript $__tool_directory__/cpm_tpm_rpk.R
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
14 -d $input
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
15 -t $option.type_transfo
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
16 -s $input_sep
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
17 -c $input_header
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
18 #if $option.type_transfo == "tpm":
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
19 -f $option.gene_file
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
20 --gene_sep $option.gene_sep
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
21 --gene_header $option.gene_header
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
22 #end if
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
23 #if $option.type_transfo == "rpk":
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
24 -f $option.gene_file
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
25 --gene_sep $option.gene_sep
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
26 --gene_header $option.gene_header
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
27 #end if
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
28 -l $log
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
29 #if $log == "FALSE":
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
30 -o ${output}
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
31 #else if $log == "TRUE":
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
32 -o ${output_log}
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
33 #end if
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
34 #if $visu_option.visualisation == "yes":
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
35 --visu 'TRUE'
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
36 #if $visu_option.tsne_labels == "yes":
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
37 --tsne_labels 'TRUE'
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
38 #else
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
39 --tsne_labels 'FALSE'
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
40 #end if
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
41 --seed '$visu_option.seed'
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
42 --perp '$visu_option.perp'
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
43 --theta '$visu_option.theta'
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
44 --tsne_out '$tsne_out'
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
45 --pca_out '$pca_out'
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
46 #end if
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
47 ]]></command>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
48 <inputs>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
49 <param name="input" type="data" format="txt" label="Raw counts of expression data"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
50 <param name="input_sep" type="select" label="Input column separator">
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
51 <option value="tab" selected="true">Tabs</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
52 <option value=",">Comma</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
53 <option value="\ ">Whitespace</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
54 <option value=".">Dots</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
55 <option value="_">Underscores</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
56 <option value="-">Dashes</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
57 </param>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
58 <param name="input_header" type="select" label="Consider first line of input file as header?">
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
59 <option value="TRUE" selected="true">Yes</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
60 <option value="FALSE">No</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
61 </param>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
62 <conditional name="option">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
63 <param name="type_transfo" type="select" label="Type of transformation">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
64 <option value="cpm" selected="true">CPM</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
65 <option value="tpm">TPM</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
66 <option value="rpk">RPK</option>
3
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
67 <option value="none">NONE</option>
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
68 </param>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
69 <when value="tpm">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
70 <param name="gene_file" type="data" format="txt" label="Gene length file"/>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
71 <param name="gene_sep" type="select" label="Gene length column separator">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
72 <option value="tab" selected="true">Tabs</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
73 <option value=",">Commas</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
74 <option value="\ ">Whitespaces</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
75 <option value=".">Dots</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
76 <option value="_">Underscores</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
77 <option value="-">Dashes</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
78 </param>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
79 <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
80 <option value="TRUE" selected="true">Yes</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
81 <option value="FALSE">No</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
82 </param>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
83 </when>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
84 <when value="rpk">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
85 <param name="gene_file" type="data" format="txt" label="Gene length file"/>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
86 <param name="gene_sep" type="select" label="Gene length column separator">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
87 <option value="tab" selected="true">Tabs</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
88 <option value=",">Commas</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
89 <option value="\ ">Whitespaces</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
90 <option value=".">Dots</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
91 <option value="_">Underscores</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
92 <option value="-">Dashes</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
93 </param>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
94 <param name="gene_header" type="select" label="Consider first line of gene length file as header ?">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
95 <option value="TRUE" selected="true">Yes</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
96 <option value="FALSE">No</option>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
97 </param>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
98 </when>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
99 <when value="cpm">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
100 </when>
3
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
101 <when value="none">
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
102 </when>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
103 </conditional>
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
104 <param name="log" type="select" label="Data should be log transformed ?">
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
105 <option value="FALSE" selected="true">No</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
106 <option value="TRUE">Yes</option>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
107 </param>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
108 <conditional name="visu_option">
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
109 <param name="visualisation" type="select" label="Visualisation of data with various dimensionality reduction methods" >
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
110 <option value="no" selected="true">No visualisation</option>
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
111 <option value="yes" >t-SNE and PCA</option>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
112 </param>
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
113 <when value="yes">
3
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
114 <param name="seed" value="49.0" type="float" label="Seed value for reproducibility of t-SNE" help="Set to 49 as default" />
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
115 <param name="perp" value="10.0" type="float" label="perplexity (t-SNE)" help="should be less than ((nbre observations)-1)/3" />
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
116 <param name="theta" value="1.0" type="float" label="theta (t-SNE)"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
117 <param name="tsne_labels" type="select" label="Add labels to points plots" >
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
118 <option value="no" selected="true">No Labels</option>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
119 <option value="yes" >Label points</option>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
120 </param>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
121 </when>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
122 <when value="no" />
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
123 </conditional>
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
124 </inputs>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
125 <outputs>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
126 <data name="output" format="tabular" label="${option.type_transfo} from ${on_string}">
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
127 <filter>log == "FALSE"</filter>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
128 </data>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
129 <data name="output_log" format="tabular" label="log2(${option.type_transfo} +1) from ${on_string}">
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
130 <filter>log == "TRUE"</filter>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
131 </data>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
132 <data name="tsne_out" format="pdf" label="tsne from ${on_string}">
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
133 <filter>visu_option['visualisation'] == 'yes'</filter>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
134 </data>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
135 <data name="pca_out" format="pdf" label="PCA from ${on_string}">
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
136 <filter>visu_option['visualisation'] == 'yes'</filter>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
137 </data>
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
138 </outputs>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
139 <tests>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
140 <!-- test t-SNE -->
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
141 <test>
3
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
142 <param name="input" value="none.tab" ftype="tabular"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
143 <param name="type_transfo" value="none"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
144 <param name="log" value="FALSE"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
145 <param name="visualisation" value="yes"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
146 <param name="seed" value="49"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
147 <param name="perp" value="10"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
148 <param name="theta" value="1" />
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
149 <param name="tsne_labels" value="yes" />
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
150 <output name="output" file="none.tab" ftype="tabular"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
151 <output name="tsne_out" file="none_tsne.pdf" ftype="pdf"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
152 <output name="pca_out" file="none_pca.pdf" ftype="pdf"/>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
153 </test>
8b1020c25f0f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 9149001c65de633ddfd2f91cf208074e40482ce3
artbio
parents: 2
diff changeset
154 <test>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
155 <param name="input" value="counts.tab" ftype="tabular"/>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
156 <param name="type_transfo" value="cpm"/>
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
157 <param name="log" value="TRUE"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
158 <param name="visualisation" value="yes"/>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
159 <param name="seed" value="49"/>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
160 <param name="perp" value="2"/>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
161 <param name="theta" value="1" />
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
162 <param name="tsne_labels" value="yes" />
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
163 <output name="output" file="logcpm.tab" ftype="tabular"/>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
164 <output name="tsne_out" file="tsne.pdf" ftype="pdf"/>
2
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
165 <output name="pca_out" file="pca.pdf" ftype="pdf"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
166 </test>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
167 <test>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
168 <param name="input" value="counts.tab" ftype="tabular"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
169 <param name="type_transfo" value="tpm"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
170 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
171 <param name="log" value="TRUE"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
172 <param name="visualisation" value="yes"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
173 <param name="seed" value="49"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
174 <param name="perp" value="2"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
175 <param name="theta" value="1" />
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
176 <param name="tsne_labels" value="no" />
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
177 <output name="output" file="logtpm.tab" ftype="tabular"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
178 <output name="tsne_out" file="tsne.nolab.pdf" ftype="pdf"/>
563337e780ce planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit 4ade64ddb1b4e2c62cd153bee13c7ce4ff2d249d
artbio
parents: 1
diff changeset
179 <output name="pca_out" file="pca.nolab.pdf" ftype="pdf"/>
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
180 </test>
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
181 <!-- test without t-SNE -->
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
182 <test>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
183 <param name="input" value="counts.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
184 <param name="type_transfo" value="cpm"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
185 <output name="output" file="cpm.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
186 </test>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
187 <test>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
188 <param name="input" value="counts.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
189 <param name="type_transfo" value="cpm"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
190 <param name="log" value="TRUE"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
191 <output name="output" file="logcpm.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
192 </test>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
193 <test>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
194 <param name="input" value="counts.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
195 <param name="type_transfo" value="tpm"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
196 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
197 <param name="gene_header" value="TRUE"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
198 <output name="output" file="tpm.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
199 </test>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
200 <test>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
201 <param name="input" value="counts.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
202 <param name="type_transfo" value="tpm"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
203 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
204 <param name="gene_header" value="TRUE"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
205 <param name="log" value="TRUE"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
206 <output name="output" file="logtpm.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
207 </test>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
208 <test>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
209 <param name="input" value="counts.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
210 <param name="type_transfo" value="rpk"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
211 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
212 <param name="gene_header" value="TRUE"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
213 <output name="output" file="rpk.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
214 </test>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
215 <test>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
216 <param name="input" value="counts.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
217 <param name="type_transfo" value="rpk"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
218 <param name="gene_file" value="gene_length.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
219 <param name="gene_header" value="TRUE"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
220 <param name="log" value="TRUE"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
221 <output name="output" file="logrpk.tab" ftype="tabular"/>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
222 </test>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
223 </tests>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
224 <help>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
225
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
226 **What it does**
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
227
1
b74bab5157c4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit d46436d5d73356c8803d6d97a110a2754e8a03fb
artbio
parents: 0
diff changeset
228 Takes a raw count expression matrix and returns a table of normalized expression values.
0
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
229
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
230 Normalization can be:
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
231
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
232 - CPM (Counts Per Million) are obtained by dividing counts by the library counts sum and multiplying the results by a million.
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
233 - RPK (Reads Per Kilobases) are obtained by dividing read counts by gene lengths (expressed in kilo-nucleotides).
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
234 - TPM (Transcripts Per Million) are obtained by dividing RPK values by the sum of all RPK values in a sample and multiplying the results by 1 million.
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
235
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
236 RPK and TPM require a two-column correspondance table gene_name - gene length where the length is specified in nucleotide. Both these metrics are relevant only for sequencing of full length RNAs.
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
237
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
238 Note: do not comment you header line if you have header line in you tabular input (ie do not start the header line with a '#' character)
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
239
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
240 Computed values may be log-transformed (log2([CPM or RPK or TPM]+1))
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
241
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
242 </help>
35d032c46a4e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cpm_tpm_rpk commit cc0fd23c039cc4a39c5e4e320b50666b7d9b6f65
artbio
parents:
diff changeset
243 </tool>