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comparison BlastAlign.xml @ 7:9c0044eff621 draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
author abims-sbr
date Tue, 27 Feb 2018 08:47:11 -0500
parents e0bea88bb09f
children f19cca5b8632
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6:e0bea88bb09f 7:9c0044eff621
1 <tool name="BlastAlign" id="blastalign" version="2.0"> 1 <tool name="BlastAlign" id="blastalign" version="2.1">
2 2
3 <description> 3 <description>
4 Align the nucleic acid sequences using BLASTN 4 Align the nucleic acid sequences using BLASTN
5 </description> 5 </description>
6 6
33 -s $advanced_option.s 33 -s $advanced_option.s
34 #end if 34 #end if
35 && 35 &&
36 ln -s '$input.element_identifier'".fasta.phy" out.phy && 36 ln -s '$input.element_identifier'".fasta.phy" out.phy &&
37 ln -s '$input.element_identifier'".fasta.nxs" out.nxs 37 ln -s '$input.element_identifier'".fasta.nxs" out.nxs
38 #if $fasta_out.value == True 38 #if $output_format.value == "fasta"
39 && python $__tool_directory__/scripts/S01_phylip2fasta.py out.phy out.fasta 39 && python $__tool_directory__/scripts/S01_phylip2fasta.py out.phy out.fasta
40 #end if 40 #end if
41 41
42 ]]></command> 42 ]]></command>
43 <inputs> 43 <inputs>
48 <param argument="-r" type="text" area="True" size="1x20" label="Choose a reference sequence" help="default is to search for best candidate (if entered, the sequence will be extracted, written to a separate file, and blasted against the original input file)"/> 48 <param argument="-r" type="text" area="True" size="1x20" label="Choose a reference sequence" help="default is to search for best candidate (if entered, the sequence will be extracted, written to a separate file, and blasted against the original input file)"/>
49 <param argument="-x" type="text" area="True" size="5x25" label="Choose the sequences to be excluded from this analysis" help="name of comma-separated sequences " /> 49 <param argument="-x" type="text" area="True" size="5x25" label="Choose the sequences to be excluded from this analysis" help="name of comma-separated sequences " />
50 <param argument="-n" type="boolean" checked="true" truevalue="T" falsevalue="F" label="Retain original names in output files" help="option F is to output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the program" /> 50 <param argument="-n" type="boolean" checked="true" truevalue="T" falsevalue="F" label="Retain original names in output files" help="option F is to output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the program" />
51 <param argument="-s" type="integer" value="0" min="0" label="Number of sequences to be used in initial search for reference sequence" help="default (= 0) is to find the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large" /> 51 <param argument="-s" type="integer" value="0" min="0" label="Number of sequences to be used in initial search for reference sequence" help="default (= 0) is to find the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large" />
52 </section> 52 </section>
53 53
54 <param name="fasta_out" type="boolean" checked="true" label="Do you want to convert the output phylip in fasta format ? " /> 54 <param name="output_format" type="select" label="Output format" help="phylip, nexus, or fasta." >
55 <option value="fasta">fasta</option>
56 <option value="phylip">phylip</option>
57 <option value="nexus">nexus</option>
58 </param>
55 </inputs> 59 </inputs>
56 60
57 <outputs> 61 <outputs>
58 <data format="phylip" name="phy" from_work_dir="out.phy" label="Alignment of ${input.name} in phylip" hidden="True"/> 62 <data format="phylip" name="phy" from_work_dir="out.phy" label="Blastalign on ${input.name} in phylip">
59 <data format="nexus" name="nxs" from_work_dir="out.nxs" label="Alignment of ${input.name} in nexus" hidden="True"/> 63 <filter>output_format == "phylip"</filter>
60 <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Alignment of ${input.name} in fasta" hidden="True"> 64 </data>
61 <filter>fasta_out == True</filter> 65 <data format="nexus" name="nxs" from_work_dir="out.nxs" label="Blastalign on ${input.name} in nexus">
66 <filter>output_format == "nexus"</filter>
67 </data>
68 <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Blastalign on ${input.name} in fasta">
69 <filter>output_format == "fasta"</filter>
62 </data> 70 </data>
63 </outputs> 71 </outputs>
64 72
65 <tests> 73 <tests>
66 <test> 74 <test>
70 <param name="r" value="" /> 78 <param name="r" value="" />
71 <param name="x" value="" /> 79 <param name="x" value="" />
72 <param name="n" value="False" /> 80 <param name="n" value="False" />
73 <param name="s" value="0" /> 81 <param name="s" value="0" />
74 </section> 82 </section>
75 <param name="fasta_out" value="True" /> 83 <param name="output_format" value="fasta" />
76 <output name="phy" value="outputs/locus1_sp2.phy" />
77 <output name="nxs" value="outputs/locus1_sp2.nxs" />
78 <output name="fasta" value="outputs/locus1_sp2.fasta" /> 84 <output name="fasta" value="outputs/locus1_sp2.fasta" />
79 </test> 85 </test>
80 <test> 86 <test>
81 <param name="input" ftype="fasta" value="inputs/locus1_sp3.fasta" /> 87 <param name="input" ftype="fasta" value="inputs/locus1_sp3.fasta" />
82 <section name="advanced_option"> 88 <section name="advanced_option">
84 <param name="r" value="" /> 90 <param name="r" value="" />
85 <param name="x" value="" /> 91 <param name="x" value="" />
86 <param name="n" value="False" /> 92 <param name="n" value="False" />
87 <param name="s" value="0" /> 93 <param name="s" value="0" />
88 </section> 94 </section>
89 <param name="fasta_out" value="True" /> 95 <param name="output_format" value="phylip" />
90 <output name="phy" value="outputs/locus1_sp3.phy" /> 96 <output name="phy" value="outputs/locus1_sp3.phy" />
91 <output name="nxs" value="outputs/locus1_sp3.nxs" />
92 <output name="fasta" value="outputs/locus1_sp3.fasta" />
93 </test> 97 </test>
94 <test> 98 <test>
95 <param name="input" ftype="fasta" value="inputs/locus3_sp2.fasta" /> 99 <param name="input" ftype="fasta" value="inputs/locus3_sp2.fasta" />
96 <section name="advanced_option"> 100 <section name="advanced_option">
97 <param name="m" value="95" /> 101 <param name="m" value="95" />
98 <param name="r" value="" /> 102 <param name="r" value="" />
99 <param name="x" value="" /> 103 <param name="x" value="" />
100 <param name="n" value="False" /> 104 <param name="n" value="False" />
101 <param name="s" value="0" /> 105 <param name="s" value="0" />
102 </section> 106 </section>
103 <param name="fasta_out" value="False" /> 107 <param name="output_format" value="nexus" />
104 <output name="phy" value="outputs/locus3_sp2.phy" />
105 <output name="nxs" value="outputs/locus3_sp2.nxs" /> 108 <output name="nxs" value="outputs/locus3_sp2.nxs" />
106 </test> 109 </test>
107 <test> 110 <test>
108 <param name="input" ftype="fasta" value="inputs/locus8_sp2.fasta" /> 111 <param name="input" ftype="fasta" value="inputs/locus8_sp2.fasta" />
109 <section name="advanced_option"> 112 <section name="advanced_option">
111 <param name="r" value="" /> 114 <param name="r" value="" />
112 <param name="x" value="" /> 115 <param name="x" value="" />
113 <param name="n" value="False" /> 116 <param name="n" value="False" />
114 <param name="s" value="0" /> 117 <param name="s" value="0" />
115 </section> 118 </section>
116 <param name="fasta_out" value="True" /> 119 <param name="output_format" value="phylip" />
117 <output name="phy" value="outputs/locus8_sp2.phy" /> 120 <output name="phy" value="outputs/locus8_sp2.phy" />
118 <output name="nxs" value="outputs/locus8_sp2.nxs" /> 121 </test>
119 <output name="fasta" value="outputs/locus8_sp2.fasta" /> 122 <test>
123 <param name="input" ftype="fasta" value="inputs/locus8_sp2.fasta" />
124 <section name="advanced_option">
125 <param name="m" value="95" />
126 <param name="r" value="" />
127 <param name="x" value="" />
128 <param name="n" value="False" />
129 <param name="s" value="0" />
130 </section>
131 <param name="output_format" value="fasta" />
132 <output name="phy" value="outputs/locus8_sp2.fasta" />
120 </test> 133 </test>
121 134
122 <!--locus10_sp2.fasta locus1_sp3.fasta locus2_sp2.fasta locus3_sp2.fasta locus4_sp2.fasta locus5_sp2.fasta locus6_sp2.fasta locus7_sp2.fasta locus8_sp2.fasta locus9_sp2.fasta--> 135 <!--locus10_sp2.fasta locus1_sp3.fasta locus2_sp2.fasta locus3_sp2.fasta locus4_sp2.fasta locus5_sp2.fasta locus6_sp2.fasta locus7_sp2.fasta locus8_sp2.fasta locus9_sp2.fasta-->
123 </tests> 136 </tests>
124 137
169 **-s : Number of sequences to be used in initial search for reference sequence** 182 **-s : Number of sequences to be used in initial search for reference sequence**
170 integer (between 0 and total number of sequences). 183 integer (between 0 and total number of sequences).
171 Default : 0 184 Default : 0
172 Default is finding the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large. 185 Default is finding the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large.
173 186
187 ** Output format :**
188 The user have the choice between three format (only one is returned per run) : fasta, phylip, and nexus.
174 -------- 189 --------
175 190
176 **Outputs** 191 **Outputs**
192
193 The output format is
177 194
178 - 'Alignment_{input.name}_phylip' : 195 - 'Blastalign_on_{input.name}_phylip' :
179 the aligned sequences in Phylip format. 196 the aligned sequences in Phylip format.
180 197
181 - 'Alignment_{input.name}_nexus' : 198 - 'Blastalign_on_{input.name}_nexus' :
182 the aligned sequences in Nexus format. 199 the aligned sequences in Nexus format.
183 200
184 - 'Alignment_{input_file}_fasta' : 201 - 'Blastalign_on_{input_file}_fasta' :
185 the aligned sequences in Fasta format if the option "fasta format" is checked. 202 the aligned sequences in Fasta format if the option "fasta format" is checked.
186 203
187 --------- 204 ---------
188 205
189 Changelog 206 Changelog
190 --------- 207 ---------
191 208
192 **Version 2.1 - 17/01/2018** 209 **Version 2.1 - 17/01/2018**
193 210
211 - New parameter "output format"
194 - Applied some bugfixes and minor improvments 212 - Applied some bugfixes and minor improvments
195 213
196 **Version 2.0 - 21/04/2017** 214 **Version 2.0 - 21/04/2017**
197 215
198 - NEW: BlastAlign will now be launched on one file at once. Although, it will manage a Dataset Collection to deal with numerous files. 216 - NEW: BlastAlign will now be launched on one file at once. Although, it will manage a Dataset Collection to deal with numerous files.