Mercurial > repos > abims-sbr > mutcount

annotate MutCount.xml @ 10:f62c76aab669 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
author lecorguille
date Mon, 24 Sep 2018 04:34:39 -0400
parents 04a9ada73cc4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
1 <?xml version="1.0"?>
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
2
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
3 <tool name="MutCount" id="mutcount" version="2.2.0">
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
4 <description>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
5 This tool proceeds to count codons, amino acids on each species of a set of species, and then proceeds to permutation tests.
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
6 </description>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
7
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
8 <macros>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
9 <import>macros.xml</import>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
10 </macros>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
11
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
12 <requirements>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
13 <expand macro="python_required" />
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
14 <requirement type="package" version="0.20.0">pandas</requirement>
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
15 <requirement type="package" version="1.12.0">numpy</requirement>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
16 <requirement type="package" version="1.4.4">r-optparse</requirement>
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
17 </requirements>
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
18
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
19 <command>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
20 <![CDATA[
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
21
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
22 ln -s $__tool_directory__/scripts/functions.py . &&
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
23
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
24 #if str($method.method_run) == "concat" :
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
25 python '$__tool_directory__/scripts/S01a_codons_counting.py' ${method.concat_nuc} '$method.list_species' '$method.list_species_boot' $method.num_iter $method.num_sampled > ${log}
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
26 #end if
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
27
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
28 #if str($method.method_run) == "separated" :
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
29 mkdir 01_input_files &&
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
30 ln -s '$__tool_directory__/scripts/S03b_sign_test_binomial.R' . &&
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
31 #for $input in $method.sep_file
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
32 ln -s '$input' '01_input_files/$input.element_identifier';
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
33 #end for
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
34
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
35 #if str($method.format_run)== "nucleic" :
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
36 python '$__tool_directory__/scripts/S01b_extract_variable_nuc.py' ${method.sps_list} &&
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
37 #end if
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
38
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
39 #if str($method.format_run)== "proteic" :
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
40 cp '$__tool_directory__/scripts/amino_acid_properties.csv' . &&
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
41 python '$__tool_directory__/scripts/S01b_extract_variable_prot.py' ${method.sps_list} amino_acid_properties.csv &&
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
42 #end if
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
43
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
44 python '$__tool_directory__/scripts/S02b_extreme_2states.py' ${method.sps_gp1} ${method.sps_gp2} ${method.format_run}
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
45 #end if
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
46
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
47 ]]>
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
48 </command>
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
49
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
50 <inputs>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
51 <conditional name="method">
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
52 <param name="method_run" type="select" label="Which method do you want to use for this tool? ">
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
53 <option value="concat">Concatenated genes in DNA (concatenation from RAxML run)</option>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
54 <option value="separated">Set of separated genes (from ORF_Search output "output zip containing files with CDS without indel")</option>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
55 </param>
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
56
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
57 <when value="concat">
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
58 <param name="concat_nuc" type="data" format="fasta" label="Choose your fasta file in nucleic format" help="It must contain the concatenated file in NUCLEIC format from Phylogeny tool" />
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
59 <param name="list_species" type="text" size="100" label="List of species for countings" help="List the species separated with a comma (for e.g Ap,As,Ct,Gt,Yu)" />
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
60 <param name="list_species_boot" type="text" size="100" label="List of species (at least two) used for resampling" help="List the species separated with a comma (for e.g Ap,As,Ct,Gt,Yu)" />
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
61 <param name="num_iter" type="integer" value="1000" min="0" label="Number of sampled codons" help="Sets the length (in codons) of the resampled sequences"/>
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
62 <param name="num_sampled" type="integer" value="1000" min="0" label="Number of iterations" help="Sets the number of resampled sequences"/>
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
63 </when>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
64
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
65 <when value="separated">
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
66 <param name="format_run" type="select" label="Which format do you want to use for this tool (concatenation and RAxML run) ? ">
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
67 <option value="nucleic">Nucleic format</option>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
68 <option value="proteic">Proteic format</option>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
69 </param>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
70 <param name="sep_file" type="data" format="fasta" multiple="true" label="Choose fasta files" help="Fasta files from ORF_search tool ; in nucleic or proteic, according to the format chosen above" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
71 <param name="sps_list" type="text" size="100" label="Enter all the studied species" help="Enter all the species present in the set of fasta files (comma-separated abbreviated names)" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
72 <param name="sps_gp1" type="text" size="100" label="Species for group one" help="Specify species (comma-separated abbreviated names) sharing an ecological condition"/>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
73 <param name="sps_gp2" type="text" size="100" label="Species for group two" help="Specify species (comma-separated abbreviated names) sharing an other ecological condition"/>
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
74 </when>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
75 </conditional>
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
76 </inputs>
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
77
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
78 <outputs>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
79 <!-- output concat -->
8
705a7bf4c311 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 10673955482e3c7641d9c2228265b6b69fcba4b8
abims-sbr
parents: 7
diff changeset
80 <data format="txt" name="log" label="MutCount_concat_log.output" >
705a7bf4c311 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 10673955482e3c7641d9c2228265b6b69fcba4b8
abims-sbr
parents: 7
diff changeset
81 <filter>(method['method_run']=='concat')</filter>
705a7bf4c311 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 10673955482e3c7641d9c2228265b6b69fcba4b8
abims-sbr
parents: 7
diff changeset
82 </data>
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
83 <data format="csv" name="codons_freqs" label="codons_freqs.csv" from_work_dir="codons_freqs.csv" >
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
84 <filter>(method['method_run']=='concat')</filter>
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
85 </data>
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
86 <data format="csv" name="aa_freqs" label="aa_freqs.csv" from_work_dir="aa_freqs.csv" >
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
87 <filter>(method['method_run']=='concat')</filter>
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
88 </data>
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
89 <data format="csv" name="aatypes_freqs" label="aatypes_freqs.csv" from_work_dir="aatypes_freqs.csv" >
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
90 <filter>(method['method_run']=='concat')</filter>
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
91 </data>
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
92 <data format="csv" name="gc_and_others_freqs" label="gc_and_others_freqs.csv" from_work_dir="gc_and_others_freqs.csv" >
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
93 <filter>(method['method_run']=='concat')</filter>
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
94 </data>
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
95 <data format="csv" name="codons_transitions_freqs" label="codons_transitions_freqs" from_work_dir="codons_transitions_freqs.csv" >
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
96 <filter>(method['method_run']=='concat')</filter>
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
97 </data>
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
98 <data format="csv" name="aa_transitions_freqs" label="aa_transitions_freqs.csv" from_work_dir="aa_transitions_freqs.csv" >
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
99 <filter>(method['method_run']=='concat')</filter>
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
100 </data>
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
101 <data format="csv" name="aatypes_transitions_freqs" label="aatypes_transitions.csv" from_work_dir="aatypes_transitions_freqs.csv" >
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
102 <filter>(method['method_run']=='concat')</filter>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
103 </data>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
104
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
105 <!-- outputs separated - nucleic -->
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
106 <collection name="tables_nuc" type="list" label="counts_on_nucleotides">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
107 <discover_datasets pattern="__name_and_ext__" directory="02_tables_per_nucleotide" />
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
108 <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
109 </collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
110 <collection name="tables_nuc_var" type="list" label="counts_on_nuc_variables">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
111 <discover_datasets pattern="__name_and_ext__" directory="02_tables_per_nuc_variable" />
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
112 <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
113 </collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
114 <collection name="outputs_nuc" type="list" label="binomial_tests_on_nucleotides">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
115 <discover_datasets pattern="__name_and_ext__" directory="04_outputs_nucleotides" />
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
116 <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
117 </collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
118 <collection name="outputs_nuc_var" type="list" label="binomial_tests_on_nuc_variables">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
119 <discover_datasets pattern="__name_and_ext__" directory="04_outputs_nuc_variables" />
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
120 <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
121 </collection>
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
122
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
123 <!-- outputs separated - proteic -->
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
124 <collection name="tables_aa" type="list" label="counts_on_amino_acids">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
125 <discover_datasets pattern="__name_and_ext__" directory="02_tables_per_aa" />
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
126 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
127 </collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
128 <collection name="tables_variables" type="list" label="counts_on_indices">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
129 <discover_datasets pattern="__name_and_ext__" directory="02_tables_per_aa_variable" />
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
130 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
131 </collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
132 <collection name="outputs_aa" type="list" label="binomial_tests_on_amino_acids">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
133 <discover_datasets pattern="__name_and_ext__" directory="04_outputs_aa" />
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
134 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
135 </collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
136 <collection name="outputs_variables" type="list" label="binomial_tests_on_indices">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
137 <discover_datasets pattern="__name_and_ext__" directory="04_outputs_aa_variables" />
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
138 <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
139 </collection>
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
140 </outputs>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
141
7
f1e24200e5ae planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit b7a3030ea134b5dfad89b1a869db659d72d1145c
abims-sbr
parents: 6
diff changeset
142 <tests>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
143
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
144 <test>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
145 <conditional name="method" >
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
146 <param name="method_run" value="concat" />
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
147 <param name="concat_nuc" ftype="fasta" value="concatenation.fasta" />
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
148 <param name="list_species" ftype="text" value="Ps,Pp,Pu,Ac,Ap,Pf,Pg,Ph,Pi" />
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
149 <param name="list_species_boot" ftype="text" value="Ps,Pp,Pu,Pf" />
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
150 <param name="num_iter" value="200" />
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
151 <param name="num_sampled" value="200" />
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
152 </conditional>
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
153 <output name="log" value="OUT_concat/MutCount_concat_log.output" lines_diff="2"/>
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
154 <output name="codons_freqs" value="OUT_concat/codons_freqs.csv" lines_diff="18"/>
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
155 <output name="aa_freqs" value="OUT_concat/aa_freqs.csv" lines_diff="18"/>
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
156 <output name="aatypes_freqs" value="OUT_concat/aatypes_freqs.csv" lines_diff="18"/>
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
157 <output name="gc_and_others_freqs" value="OUT_concat/gc_and_others_freqs.csv"/>
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
158 <output name="codons_transitions_freqs" value="OUT_concat/codons_transitions_freqs.csv" lines_diff="72"/>
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
159 <output name="aa_transitions_freqs" value="OUT_concat/aa_transitions_freqs.csv" lines_diff="72"/>
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
160 <output name="aatypes_transitions_freqs" value="OUT_concat/aatypes_transitions_freqs.csv" lines_diff="72"/>
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
161 </test>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
162
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
163 <test>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
164 <conditional name="method" >
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
165 <param name="method_run" value="separated" />
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
166 <param name="format_run" value="nucleic" />
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
167 <param name="sep_file" ftype="fasta" value="sep_nuc/orthogroup_109_with_3_species.fasta,sep_nuc/orthogroup_113_with_4_species.fasta,sep_nuc/orthogroup_253_with_2_species.fasta,sep_nuc/orthogroup_283_with_2_species.fasta,sep_nuc/orthogroup_299_with_2_species.fasta,sep_nuc/orthogroup_301_with_4_species.fasta,sep_nuc/orthogroup_316_with_4_species.fasta,sep_nuc/orthogroup_335_with_4_species.fasta,sep_nuc/orthogroup_343_with_4_species.fasta,sep_nuc/orthogroup_368_with_4_species.fasta,sep_nuc/orthogroup_404_with_4_species.fasta,sep_nuc/orthogroup_442_with_4_species.fasta,sep_nuc/orthogroup_487_with_4_species.fasta,sep_nuc/orthogroup_508_with_4_species.fasta,sep_nuc/orthogroup_544_with_4_species.fasta,sep_nuc/orthogroup_546_with_4_species.fasta,sep_nuc/orthogroup_588_with_4_species.fasta,sep_nuc/orthogroup_623_with_4_species.fasta,sep_nuc/orthogroup_651_with_4_species.fasta,sep_nuc/orthogroup_660_with_4_species.fasta,sep_nuc/orthogroup_696_with_4_species.fasta,sep_nuc/orthogroup_707_with_4_species.fasta,sep_nuc/orthogroup_727_with_4_species.fasta,sep_nuc/orthogroup_761_with_4_species.fasta" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
168 <param name="sps_list" value="Ha,Lf,Bs,Bj" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
169 <param name="sps_gp1" value="Ha,Lf" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
170 <param name="sps_gp2" value="Bs,Bj" />
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
171 </conditional>
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
172 <output_collection name="tables_nuc" type="list" count="4">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
173 <element name="A" file="OUT_nuc/02_tables_per_nucleotide/A.csv" ftype="csv" compare="diff" lines_diff="8" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
174 <element name="C" file="OUT_nuc/02_tables_per_nucleotide/C.csv" ftype="csv" compare="diff" lines_diff="8" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
175 <element name="G" file="OUT_nuc/02_tables_per_nucleotide/G.csv" ftype="csv" compare="diff" lines_diff="8" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
176 <element name="T" file="OUT_nuc/02_tables_per_nucleotide/T.csv" ftype="csv" compare="diff" lines_diff="8" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
177 </output_collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
178 <output_collection name="tables_nuc_var" type="list" count="8">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
179 <element name="DIFF_AT" file="OUT_nuc/02_tables_per_nuc_variable/DIFF_AT.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
180 <element name="DIFF_GC" file="OUT_nuc/02_tables_per_nuc_variable/DIFF_GC.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
181 <!--
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
182 <element name="GC_percent" file="OUT_nuc/02_tables_per_nuc_variable/_GC_percent.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
183 -->
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
184 <element name="PLI_AT" file="OUT_nuc/02_tables_per_nuc_variable/PLI_AT.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
185 <element name="PLI_AT_1000" file="OUT_nuc/02_tables_per_nuc_variable/PLI_AT_1000.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
186 <element name="PLI_GC" file="OUT_nuc/02_tables_per_nuc_variable/PLI_GC.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
187 <element name="PLI_GC_1000" file="OUT_nuc/02_tables_per_nuc_variable/PLI_GC_1000.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
188 <element name="purine_percent" file="OUT_nuc/02_tables_per_nuc_variable/purine_percent.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
189 </output_collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
190 <output_collection name="outputs_nuc" type="list" count="4">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
191 <element name="A" file="OUT_nuc/04_outputs_nucleotides/A.csv" ftype="csv" compare="diff" lines_diff="8" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
192 <element name="C" file="OUT_nuc/04_outputs_nucleotides/C.csv" ftype="csv" compare="diff" lines_diff="8" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
193 <element name="G" file="OUT_nuc/04_outputs_nucleotides/G.csv" ftype="csv" compare="diff" lines_diff="8" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
194 <element name="T" file="OUT_nuc/04_outputs_nucleotides/T.csv" ftype="csv" compare="diff" lines_diff="8" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
195 </output_collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
196 <output_collection name="outputs_nuc_var" type="list" count="8">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
197 <element name="DIFF_AT" file="OUT_nuc/04_outputs_nuc_variables/DIFF_AT.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
198 <element name="DIFF_GC" file="OUT_nuc/04_outputs_nuc_variables/DIFF_GC.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
199 <!--
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
200 <element name="GC_percent" file="OUT_nuc/04_outputs_nuc_variables/GC_percent.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
201 -->
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
202 <element name="PLI_AT" file="OUT_nuc/04_outputs_nuc_variables/PLI_AT.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
203 <element name="PLI_AT_1000" file="OUT_nuc/04_outputs_nuc_variables/PLI_AT_1000.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
204 <element name="PLI_GC" file="OUT_nuc/04_outputs_nuc_variables/PLI_GC.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
205 <element name="PLI_GC_1000" file="OUT_nuc/04_outputs_nuc_variables/PLI_GC_1000.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
206 <element name="purine_percent" file="OUT_nuc/04_outputs_nuc_variables/purine_percent.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
207 </output_collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
208 </test>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
209
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
210 <test>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
211 <conditional name="method" >
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
212 <param name="method_run" value="separated" />
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
213 <param name="format_run" value="proteic" />
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
214 <param name="sep_file" ftype="fasta" value="sep_aa/locus_3sp_2.fasta,sep_aa/locus_3sp_7.fasta,sep_aa/locus_4sp_4.fasta,sep_aa/locus_4sp_6.fasta,sep_aa/locus_6sp_10.fasta,sep_aa/locus_6sp_11.fasta,sep_aa/locus_6sp_16.fasta,sep_aa/locus_6sp_18.fasta,sep_aa/locus_6sp_25.fasta,sep_aa/locus_6sp_27.fasta,sep_aa/locus_6sp_30.fasta,sep_aa/locus_6sp_32.fasta,sep_aa/locus_6sp_35.fasta,sep_aa/locus_6sp_38.fasta,sep_aa/locus_6sp_39.fasta,sep_aa/locus_6sp_40.fasta,sep_aa/locus_6sp_41.fasta,sep_aa/locus_6sp_46.fasta,sep_aa/locus_6sp_47.fasta,sep_aa/locus_6sp_50.fasta,sep_aa/locus_6sp_53.fasta,sep_aa/locus_6sp_57.fasta,sep_aa/locus_6sp_58.fasta,sep_aa/locus_6sp_60.fasta" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
215 <param name="sps_list" value="Ps,Pp,Pf,Ac,Pg,Ap" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
216 <param name="sps_gp1" value="Pp,Pg" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
217 <param name="sps_gp2" value="Ap,Ps" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
218 </conditional>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
219 <output_collection name="tables_aa" type="list" count="20">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
220 <element name="A" file="OUT_aa/02_tables_per_aa/A.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
221 <element name="C" file="OUT_aa/02_tables_per_aa/C.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
222 <element name="D" file="OUT_aa/02_tables_per_aa/D.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
223 <element name="E" file="OUT_aa/02_tables_per_aa/E.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
224 <element name="F" file="OUT_aa/02_tables_per_aa/F.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
225 <element name="G" file="OUT_aa/02_tables_per_aa/G.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
226 <element name="H" file="OUT_aa/02_tables_per_aa/H.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
227 <element name="I" file="OUT_aa/02_tables_per_aa/I.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
228 <element name="K" file="OUT_aa/02_tables_per_aa/K.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
229 <element name="L" file="OUT_aa/02_tables_per_aa/L.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
230 <element name="M" file="OUT_aa/02_tables_per_aa/M.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
231 <element name="N" file="OUT_aa/02_tables_per_aa/N.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
232 <element name="P" file="OUT_aa/02_tables_per_aa/P.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
233 <element name="Q" file="OUT_aa/02_tables_per_aa/Q.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
234 <element name="R" file="OUT_aa/02_tables_per_aa/R.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
235 <element name="S" file="OUT_aa/02_tables_per_aa/S.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
236 <element name="T" file="OUT_aa/02_tables_per_aa/T.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
237 <element name="V" file="OUT_aa/02_tables_per_aa/V.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
238 <element name="W" file="OUT_aa/02_tables_per_aa/W.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
239 <element name="Y" file="OUT_aa/02_tables_per_aa/Y.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
240 </output_collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
241 <output_collection name="tables_variables" type="list" count="26">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
242
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
243 <element name="AC" file="OUT_aa/02_tables_per_aa_variable/AC.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
244 <element name="APGC" file="OUT_aa/02_tables_per_aa_variable/APGC.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
245 <element name="AVLIM" file="OUT_aa/02_tables_per_aa_variable/AVLIM.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
246 <element name="AVLIMFYW" file="OUT_aa/02_tables_per_aa_variable/AVLIMFYW.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
247 <element name="DE" file="OUT_aa/02_tables_per_aa_variable/DE.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
248 <element name="DNQTSHA" file="OUT_aa/02_tables_per_aa_variable/DNQTSHA.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
249 <element name="EK" file="OUT_aa/02_tables_per_aa_variable/EK.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
250 <element name="ERK" file="OUT_aa/02_tables_per_aa_variable/ERK.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
251 <element name="FYMINK" file="OUT_aa/02_tables_per_aa_variable/FYMINK.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
252 <element name="FYW" file="OUT_aa/02_tables_per_aa_variable/FYW.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
253 <element name="GARP" file="OUT_aa/02_tables_per_aa_variable/GARP.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
254 <element name="IVYWREL" file="OUT_aa/02_tables_per_aa_variable/IVYWREL.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
255 <element name="QH" file="OUT_aa/02_tables_per_aa_variable/QH.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
256 <element name="ratio_AC_VLIM" file="OUT_aa/02_tables_per_aa_variable/ratio_AC_VLIM.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
257 <element name="ratio_APGC_VLIM" file="OUT_aa/02_tables_per_aa_variable/ratio_APGC_VLIM.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
258 <element name="ratio_EK_QH" file="OUT_aa/02_tables_per_aa_variable/ratio_EK_QH.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
259 <element name="ratio_ERK_DNQTSHA" file="OUT_aa/02_tables_per_aa_variable/ratio_ERK_DNQTSHA.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
260 <element name="ratio_GARP_FYMINK" file="OUT_aa/02_tables_per_aa_variable/ratio_GARP_FYMINK.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
261 <element name="RHK" file="OUT_aa/02_tables_per_aa_variable/RHK.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
262 <element name="RHKDE" file="OUT_aa/02_tables_per_aa_variable/RHKDE.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
263 <element name="STNQ" file="OUT_aa/02_tables_per_aa_variable/STNQ.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
264 <!--
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
265 <element name="total_hydratation" file="OUT_aa/02_tables_per_aa_variable/total_hydratation.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
266 -->
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
267 <element name="total_partial_specific_volume" file="OUT_aa/02_tables_per_aa_variable/total_partial_specific_volume.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
268 <element name="total_residue_volume" file="OUT_aa/02_tables_per_aa_variable/total_residue_volume.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
269 <element name="total_residue_weight" file="OUT_aa/02_tables_per_aa_variable/total_residue_weight.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
270 <element name="VLIM" file="OUT_aa/02_tables_per_aa_variable/VLIM.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
271 </output_collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
272 <output_collection name="outputs_aa" type="list" count="20">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
273 <element name="A" file="OUT_aa/04_outputs_aa/A.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
274 <element name="C" file="OUT_aa/04_outputs_aa/C.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
275 <element name="D" file="OUT_aa/04_outputs_aa/D.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
276 <element name="E" file="OUT_aa/04_outputs_aa/E.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
277 <element name="F" file="OUT_aa/04_outputs_aa/F.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
278 <element name="G" file="OUT_aa/04_outputs_aa/G.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
279 <element name="H" file="OUT_aa/04_outputs_aa/H.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
280 <element name="I" file="OUT_aa/04_outputs_aa/I.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
281 <element name="K" file="OUT_aa/04_outputs_aa/K.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
282 <element name="L" file="OUT_aa/04_outputs_aa/L.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
283 <element name="M" file="OUT_aa/04_outputs_aa/M.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
284 <element name="N" file="OUT_aa/04_outputs_aa/N.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
285 <element name="P" file="OUT_aa/04_outputs_aa/P.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
286 <element name="Q" file="OUT_aa/04_outputs_aa/Q.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
287 <element name="R" file="OUT_aa/04_outputs_aa/R.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
288 <element name="S" file="OUT_aa/04_outputs_aa/S.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
289 <element name="T" file="OUT_aa/04_outputs_aa/T.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
290 <element name="V" file="OUT_aa/04_outputs_aa/V.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
291 <element name="W" file="OUT_aa/04_outputs_aa/W.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
292 <element name="Y" file="OUT_aa/04_outputs_aa/Y.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
293 </output_collection>
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
294 <output_collection name="outputs_variables" type="list" count="26">
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
295 <element name="AC" file="OUT_aa/04_outputs_aa_variables/AC.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
296 <element name="APGC" file="OUT_aa/04_outputs_aa_variables/APGC.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
297 <element name="AVLIM" file="OUT_aa/04_outputs_aa_variables/AVLIM.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
298 <element name="AVLIMFYW" file="OUT_aa/04_outputs_aa_variables/AVLIMFYW.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
299 <element name="DE" file="OUT_aa/04_outputs_aa_variables/DE.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
300 <element name="DNQTSHA" file="OUT_aa/04_outputs_aa_variables/DNQTSHA.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
301 <element name="EK" file="OUT_aa/04_outputs_aa_variables/EK.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
302 <element name="ERK" file="OUT_aa/04_outputs_aa_variables/ERK.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
303 <element name="FYMINK" file="OUT_aa/04_outputs_aa_variables/FYMINK.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
304 <element name="FYW" file="OUT_aa/04_outputs_aa_variables/FYW.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
305 <element name="GARP" file="OUT_aa/04_outputs_aa_variables/GARP.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
306 <element name="IVYWREL" file="OUT_aa/04_outputs_aa_variables/IVYWREL.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
307 <element name="QH" file="OUT_aa/04_outputs_aa_variables/QH.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
308 <element name="ratio_AC_VLIM" file="OUT_aa/04_outputs_aa_variables/ratio_AC_VLIM.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
309 <element name="ratio_APGC_VLIM" file="OUT_aa/04_outputs_aa_variables/ratio_APGC_VLIM.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
310 <element name="ratio_EK_QH" file="OUT_aa/04_outputs_aa_variables/ratio_EK_QH.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
311 <element name="ratio_ERK_DNQTSHA" file="OUT_aa/04_outputs_aa_variables/ratio_ERK_DNQTSHA.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
312 <element name="ratio_GARP_FYMINK" file="OUT_aa/04_outputs_aa_variables/ratio_GARP_FYMINK.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
313 <element name="RHK" file="OUT_aa/04_outputs_aa_variables/RHK.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
314 <element name="RHKDE" file="OUT_aa/04_outputs_aa_variables/RHKDE.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
315 <element name="STNQ" file="OUT_aa/04_outputs_aa_variables/STNQ.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
316 <!--
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
317 <element name="total_hydratation" file="OUT_aa/04_outputs_aa_variables/total_hydratation.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
318 -->
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
319 <element name="total_partial_specific_volume" file="OUT_aa/04_outputs_aa_variables/total_partial_specific_volume.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
320 <element name="total_residue_volume" file="OUT_aa/04_outputs_aa_variables/total_residue_volume.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
321 <element name="total_residue_weight" file="OUT_aa/04_outputs_aa_variables/total_residue_weight.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
322 <element name="VLIM" file="OUT_aa/04_outputs_aa_variables/VLIM.csv" ftype="csv" compare="diff" lines_diff="6" />
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
323 </output_collection>
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
324 </test>
9
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 8
diff changeset
325
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
326 </tests>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
327
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
328 <help>
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
329
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
330 @HELP_AUTHORS@
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
331
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
332 <![CDATA[
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
333
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
334 **Description**
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
335
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
336 *1-Separated mode*
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
337
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
338 Input files are all the orthogroups computed by the AdaptSearch suite; Counts and test are computed on each group separatly. This mode counts occurrences of amino-acids or nucleic acids, according to the sequences type, in each distinct orthogroup. Then, two subgroups of species are set by the user :
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
339
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
340 - A first group, constitued by species having something in common (an ecological trait, an ecological niche, a particular environmental adaptation)
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
341 - A second group, constitued by species sharing the opposite trait (for example, the user can have a first subgroup made with species adapted to high temperatures and a second group made with species adapted to cold temperatures)
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
342
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
343 Within the groups, the program checks wether the occurrences of each element (amino-acid, nucleic acid, thermostability indice, GC content …) is higher of lower between one species and all the species of the opposite group. Binomial tests are then performed of these counts.
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
344
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
345 *2-Concatenated mode*
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
346
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
347 The input file is the super-alignment obtained by concatenation of all the orthogroups computed by the AdaptSearch suite. This script counts the number of codons, amino acids, and types of amino acids in sequences, as well as the mutation bias from one item to another between 2 sequences. Counts are then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences.
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
348
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
349 In the output files, the pvalues indicate the position of the observed data in a distribution of empirical counts obtained from a resampling of the data. Values above 0.95 indicate a significantly higher count, values under 0.05 a significantly lower count.
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
350
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
351 The script resamples random pairs of aligned codon to determine what counts can be expected under the hypothesis of an homogenous dataset.
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
352 Counts are performed on each generated random alignement, thousands of alignments allow to draw a gaussian distribution of the counts.
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
353 Then the script simply checks whether the observed data are within the 5% lowest or 5% highest values of the distribution.
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
354
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
355 --------
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
356
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
357 .. class:: infomark
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
358
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
359 **Input files**
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
360
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
361 If you choose the concatenated method, the input file is the concatenated genes fasta file (in nucleic format) from a previous run of the toolConcatPhyl.
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
362
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
363 If you choose the separated method, there are two input files :
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
364 - A dataset collection containing output files from the CDS_Search tool, the one without indels. These files must be in nucleic or proteic format according to the format chosen along with the method.
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
365 - The concatenated genes fasta file from ConcatPhyl, only used here to retrieve species name.
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
366
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
367 --------
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
368
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
369 **Parameters**
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
370
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
371 There are parameters only for the "Concatenated" method :
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
372
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
373 - The list of species for **countings**, separated by commas and without space (e.g : sp1,sp2,sp3,sp4). You can run the tool on subgroup of species, not only on the total number of species present in the previous tools.
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
374
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
375 - The list of species for **resampling**, separated by commas and without space (e.g : sp1,sp2,sp3,sp4). You can run the tool on subgroup of species (at least two species), not only on the total number of species present in the previous tools.
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
376
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
377 - The number of iterations : the number of alignments that will be generated (effect on the resolution of the gaussian distribution). Shouldn't be lower than 1000 to have a relatively smooth gaussian distribution.
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
378
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
379 - The number of sampled codons : the number of pairs of codons in each generated alignments (effect on the robustness on the counts performed on this alignement). Shouldn't be lower than 1000 to detect codons with relatively low occurence (<1%).
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
380
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
381 --------
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
382
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
383 **Outputs**
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
384
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
385 Many outputs in .csv format , varying according to the chosen method and format (separated, nucleic ...)
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
386 - When method = concat : 6 .csv outputs : countings of codons, amino acids, amino acids types, and transitions from amino acid to amino acid and from amino acid type to amino acid type.
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
387 - When method = separated and format = nucleic : 4 collections with several .csv files : counts tables and binomial sign tests results for nucleotides and various indices (GC and purine percent ...) .
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
388 - When method = separated and format = proteic : 4 collections with several .csv files : counts tables and binomial sign tests results for amino-acids and various indices (thermophilic indices, hydratation, partial specific volume...).
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
389 ---------
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
390
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
391 **The AdaptSearch Pipeline**
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
392
6
fe74cf0d4e7a planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 7c9540507076087e858141f9dd5df33409690dac
abims-sbr
parents: 5
diff changeset
393 .. image:: adaptsearch_picture_helps.png
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
394
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
395 ---------
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
396
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
397 Changelog
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
398 ---------
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
399
10
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
400 **Version 2.2.0 - 10/07/2018**
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
401 - Updated separated mode : added a binomial sign test
f62c76aab669 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
lecorguille
parents: 9
diff changeset
402
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
403 **Version 2.1 - 26/02/2017**
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents: 4
diff changeset
404 - Fully re-written the concat method : fixed mistakes + cleaner code
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
405 - Splitted output of concatenated method in several csv files.
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
406 - Bug corrected in output files of separated method.
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
407
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
408 **Version 2.0 - 12/07/2017**
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
409
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
410 - NEW: Replaced the zip between tools by Dataset Collection
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
411 - More functional tests
0
78dd6454f6f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 73670b26c75bb6c1a6332481920f3036314de364
abims-sbr
parents:
diff changeset
412
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
413 **Version 1.0 - 14/04/2017**
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
414
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
415 - Added the tools to the suite
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
416 - Added a functional test with planemo
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
417 - Planemo test using conda dependencies for python
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
418 - Scripts renamed + symlinks to the directory 'scripts'
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
419
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
420 ]]>
1
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
421
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
422 </help>
8de21b6eb110 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
423
2
988467f963f0 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
424 </tool>