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comparison POGs.xml @ 8:3fbf4e4d111e draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
author abims-sbr
date Tue, 27 Feb 2018 08:41:45 -0500
parents 04422117fcd7
children a76e4758dc44
comparison
equal deleted inserted replaced
7:04422117fcd7 8:3fbf4e4d111e
14 <requirement type="package" version="1.12.0">numpy</requirement> 14 <requirement type="package" version="1.12.0">numpy</requirement>
15 </requirements> 15 </requirements>
16 16
17 <command> 17 <command>
18 <![CDATA[ 18 <![CDATA[
19 #set $infiles_from_paiwise_prot = "" 19 #set $infiles_from_paiwise_dna = ""
20 #for $input_from_paiwise_prot in $inputs_from_paiwise_prot 20 #for $input_from_paiwise_dna in $inputs_from_paiwise_dna
21 ln -s '$input_from_paiwise_prot' '$input_from_paiwise_prot.element_identifier'; 21 ln -s '$input_from_paiwise_dna' '$input_from_paiwise_dna.element_identifier';
22 #set $infiles_from_paiwise_prot = $infiles_from_paiwise_prot + $input_from_paiwise_prot.element_identifier + "," 22 #set $infiles_from_paiwise_dna = $infiles_from_paiwise_dna + $input_from_paiwise_dna.element_identifier + ","
23 #end for 23 #end for
24 #set $infiles_from_paiwise_prot = $infiles_from_paiwise_prot[:-1] 24 #set $infiles_from_paiwise_dna = $infiles_from_paiwise_dna[:-1]
25 25
26 python '$__tool_directory__/scripts/pogs.py' '$infiles_from_paiwise_prot' '$minspec' 26 python '$__tool_directory__/scripts/pogs.py' '$infiles_from_paiwise_dna' '$minspec'
27 27
28 #if '$verbose': 28 #if $verbose=="T":
29 -v 29 -v
30 #end if 30 #end if
31 #if '$paralogs': 31 #if $paralogs=="T":
32 -p 32 -p
33 #end if 33 #end if
34 34
35 > ${log} 35 > ${log}
36 36
37 ]]> 37 ]]>
38 </command> 38 </command>
39 39
40 <inputs> 40 <inputs>
41 <param name="inputs_from_paiwise_prot" type="data" format="fasta" multiple="true" label="Input files from Pairwise Prot" /> 41 <param name="inputs_from_paiwise_dna" type="data" format="fasta" multiple="true" label="Input files from Pairwise DNA" />
42 <param name="minspec" type="integer" value="3" label="Drop orthogroups with less than n species" /> 42 <param name="minspec" type="integer" value="3" label="Drop orthogroups with less than n species" />
43 <param name="verbose" type="boolean" checked="True" truevalue="T" falsevalue="F" label="Verbose" help="Display a summary table of orthogroups before paralogs filtering"/> 43 <param name="verbose" type="boolean" checked="True" truevalue="T" falsevalue="F" label="Verbose" help="Display a summary table of orthogroups before paralogs filtering"/>
44 <param name="paralogs" type="boolean" checked="False" truevalue="T" falsevalue="F" label="Paralogs" help="Return also orthogroups without paralogs filtering"/> 44 <param name="paralogs" type="boolean" checked="False" truevalue="T" falsevalue="F" label="Paralogs" help="Return also orthogroups without paralogs filtering"/>
45 </inputs> 45 </inputs>
46 46
55 </collection> 55 </collection>
56 </outputs> 56 </outputs>
57 57
58 <tests> 58 <tests>
59 <test> 59 <test>
60 <param name="inputs_from_paiwise_prot" ftype="fasta" value="output_pairwise/RBH_AmAmphi_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_AcAcaud.fasta,output_pairwise/RBH_TeTerlap_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_ApApomp.fasta"/> 60 <param name="inputs_from_paiwise_dna" ftype="fasta" value="output_pairwise/RBH_AmAmphi_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_AcAcaud.fasta,output_pairwise/RBH_TeTerlap_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_ApApomp.fasta"/>
61 <param name="minspec" value="3"/> 61 <param name="minspec" value="3"/>
62 <param name="verbose" value="True"/> 62 <param name="verbose" value="True"/>
63 <param name="paralogs" value="True"/> 63 <param name="paralogs" value="True"/>
64 <output name="log" value="pogs.output" /> 64 <output name="log" value="pogs.output" />
65 <output_collection name="output" type="list"> 65 <output_collection name="output" type="list">
85 <element name="orthogroup_8_with_5_sequences_withParalogs" value="outputs_withParalogs/orthogroup_8_with_5_sequences_withParalogs.fasta" /> 85 <element name="orthogroup_8_with_5_sequences_withParalogs" value="outputs_withParalogs/orthogroup_8_with_5_sequences_withParalogs.fasta" />
86 <element name="orthogroup_9_with_3_sequences_withParalogs" value="outputs_withParalogs/orthogroup_9_with_3_sequences_withParalogs.fasta" /> 86 <element name="orthogroup_9_with_3_sequences_withParalogs" value="outputs_withParalogs/orthogroup_9_with_3_sequences_withParalogs.fasta" />
87 <element name="orthogroup_10_with_4_sequences_withParalogs" value="outputs_withParalogs/orthogroup_10_with_4_sequences_withParalogs.fasta" /> 87 <element name="orthogroup_10_with_4_sequences_withParalogs" value="outputs_withParalogs/orthogroup_10_with_4_sequences_withParalogs.fasta" />
88 </output_collection> 88 </output_collection>
89 </test> 89 </test>
90 <test>
91 <param name="inputs_from_paiwise_dna" ftype="fasta" value="output_pairwise/RBH_AmAmphi_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AcAcaud.fasta,output_pairwise/RBH_ApApomp_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_AcAcaud.fasta,output_pairwise/RBH_TeTerlap_AmAmphi.fasta,output_pairwise/RBH_TeTerlap_ApApomp.fasta"/>
92 <param name="minspec" value="3"/>
93 <param name="verbose" value="True"/>
94 <param name="paralogs" value="False"/>
95 <output name="log" value="2_pogs.output" />
96 <output_collection name="output" type="list">
97 <element name="orthogroup_1_with_4_sequences" value="outputs/orthogroup_1_with_4_sequences.fasta" />
98 <element name="orthogroup_2_with_4_sequences" value="outputs/orthogroup_2_with_4_sequences.fasta" />
99 <element name="orthogroup_3_with_3_sequences" value="outputs/orthogroup_3_with_3_sequences.fasta" />
100 <element name="orthogroup_4_with_4_sequences" value="outputs/orthogroup_4_with_4_sequences.fasta" />
101 <element name="orthogroup_5_with_3_sequences" value="outputs/orthogroup_5_with_3_sequences.fasta" />
102 <element name="orthogroup_6_with_4_sequences" value="outputs/orthogroup_6_with_4_sequences.fasta" />
103 <element name="orthogroup_7_with_3_sequences" value="outputs/orthogroup_7_with_3_sequences.fasta" />
104 <element name="orthogroup_8_with_3_sequences" value="outputs/orthogroup_8_with_3_sequences.fasta" />
105 <element name="orthogroup_9_with_3_sequences" value="outputs/orthogroup_9_with_3_sequences.fasta" />
106 <element name="orthogroup_10_with_3_sequences" value="outputs/orthogroup_10_with_3_sequences.fasta" />
107 </output_collection>
108 </test>
90 </tests> 109 </tests>
91 110
92 <help> 111 <help>
93 112
94 @HELP_AUTHORS@ 113 @HELP_AUTHORS@
103 122
104 -------- 123 --------
105 124
106 **Inputs** 125 **Inputs**
107 126
108 The output (nucleic format) of the tool 'Pairwise' (AdaptSearch suite), which consists in lists of homologous sequences between pairs of species obtained by RBH comparisons. 127 The output of the tool 'Pairwise' (pairwise_DNA, nucleic format) (AdaptSearch suite), which consists in lists of homologous sequences between pairs of species obtained by RBH comparisons.
109 128
110 -------- 129 --------
111 130
112 **Parameters** 131 **Parameters**
113 132
114 ** Species minimum ** : drop orthogroups with less than n species : orthogroups with less than n species within won't be recorded. 133 - Species minimum : drop orthogroups with less than n species : orthogroups with less than n species within won't be recorded.
115 ** verbose ** : check 'Yes' if you want a supplementary table : countings of orthogroups before the paralogous sequences removal
116 ** paralogs ** : check 'yes' if you also want to retrieve the orthogroups before the paralogous sequences removal
117 134
118 .. class:: warningmark 135 - verbose : check 'Yes' if you want a supplementary table : countings of orthogroups before the paralogous sequences removal.
136
137 - paralogs : check 'Yes' if you also want to retrieve the orthogroups before the paralogous sequences removal.
138
139 :: .. class:: warningmark
119 The minimum number of species per group only applies to the main output files. In the case of the 'paralogs' option, this parameter is more likely the minimum amount of sequences to keep. 140 The minimum number of species per group only applies to the main output files. In the case of the 'paralogs' option, this parameter is more likely the minimum amount of sequences to keep.
120 141
121 -------- 142 --------
122 143
123 **Outputs** 144 **Outputs**