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comparison t_coffee.xml @ 7:0a189243186d draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
author earlhaminst
date Wed, 18 Sep 2019 06:37:40 -0400
parents c67bd5acbae2
children ae69d14b6fbf
comparison
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6:c67bd5acbae2 7:0a189243186d
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" level="fatal" /> 7 <exit_code range="1:" level="fatal" />
8 </stdio> 8 </stdio>
9 <version_command> 9 <version_command>
10 t_coffee -version | grep Version 10 t_coffee -version | grep Version
11 </version_command> 11 </version_command>
12 <command use_shared_home="false"> 12 <command use_shared_home="false"><![CDATA[
13 <![CDATA[ 13 #if str($input_type.filter_fasta) == 'yes'
14 #if str($input_type.filter_fasta) == 'yes' 14 #set $input = 'temp.fasta'
15 #set $input = 'temp.fasta' 15 python '$__tool_directory__/filter_by_fasta_ids.py' '$input_type.identifiers' '$input_type.fasta_input' > temp.fasta &&
16 python '$__tool_directory__/filter_by_fasta_ids.py' '$input_type.identifiers' '$input_type.fasta_input' > temp.fasta && 16 #end if
17
18 #set $method_opt = ''
19 #if $method01
20 #set $method_opt += str($method01) + ','
21 #end if
22 #if $method02
23 #set $method_opt += str($method02) + ','
24 #end if
25 #if $method03
26 #set $method_opt += str($method03) + ','
27 #end if
28 #if $method_opt
29 #set $method_opt = '-method ' + $method_opt[:-1]
30 #end if
31
32 #set $output_opt = ''
33 #if $outputs
34 #set $outputs_arr = str($outputs).split(',')
35 #for $o in $outputs_arr
36 #if $o != 'dnd'
37 #set $output_opt += $o + ','
17 #end if 38 #end if
39 #end for
40 #else
41 #set $outputs_arr = []
42 #end if
43 #if $output_opt
44 #set $output_opt = '-output ' + $output_opt[:-1]
45 #end if
18 46
19 #set $method_opt = '' 47 t_coffee '$input' $method_opt $output_opt -n_core \${GALAXY_SLOTS:-1} -run_name t_coffee_out -quiet
20 #if $method01 48 ]]></command>
21 #set $method_opt += str($method01) + ','
22 #end if
23 #if $method02
24 #set $method_opt += str($method02) + ','
25 #end if
26 #if $method03
27 #set $method_opt += str($method03) + ','
28 #end if
29 #if $method_opt
30 #set $method_opt = '-method ' + $method_opt[:-1]
31 #end if
32
33 #set $output_opt = ''
34 #if $outputs
35 #set $outputs_arr = str($outputs).split(',')
36 #for $o in $outputs_arr
37 #if $o != 'dnd'
38 #set $output_opt += $o + ','
39 #end if
40 #end for
41 #else
42 #set $outputs_arr = []
43 #end if
44 #if $output_opt
45 #set $output_opt = '-output ' + $output_opt[:-1]
46 #end if
47
48 t_coffee '$input' $method_opt $output_opt -n_core \${GALAXY_SLOTS:-1} -run_name t_coffee_out -quiet
49 ]]>
50 </command>
51 <inputs> 49 <inputs>
52 <conditional name="input_type"> 50 <conditional name="input_type">
53 <param name="filter_fasta" type="select" label="Filter FASTA input?"> 51 <param name="filter_fasta" type="select" label="Filter FASTA input?">
54 <option value="no">No</option> 52 <option value="no">No</option>
55 <option value="yes">Yes</option> 53 <option value="yes">Yes</option>
145 <param name="method02" value="clustalw_msa" /> 143 <param name="method02" value="clustalw_msa" />
146 <param name="outputs" value="fasta_aln" /> 144 <param name="outputs" value="fasta_aln" />
147 <output name="fasta_aln" file="output2.fasta" ftype="fasta" /> 145 <output name="fasta_aln" file="output2.fasta" ftype="fasta" />
148 </test> 146 </test>
149 </tests> 147 </tests>
150 <help> 148 <help><![CDATA[
151 **What it does** 149 **What it does**
152 150
153 This tool is a wrapper for the T-Coffee multiple sequence alignment suite. The input is a set of sequences in FASTA format. Apart from running on the complete FASTA input, it can also run on a subset of sequences by providing a list of the FASTA IDs. 151 This tool is a wrapper for the T-Coffee multiple sequence alignment suite. The input is a set of sequences in FASTA format. Apart from running on the complete FASTA input, it can also run on a subset of sequences by providing a list of the FASTA IDs.
154 152
155 This wrapper offers selected advanced T-Coffee options like the selection of the alignment methods to use: ''Pairwise Structual Method'', ''Multiple Sequence Alignment Methods'' or ''Pairwise Sequence Alignment Methods''. 153 This wrapper offers selected advanced T-Coffee options like the selection of the alignment methods to use: ''Pairwise Structual Method'', ''Multiple Sequence Alignment Methods'' or ''Pairwise Sequence Alignment Methods''.
190 DR-----------VRK--KSGAAWQGQIVGWYCTNLTPEGYAVE------ 188 DR-----------VRK--KSGAAWQGQIVGWYCTNLTPEGYAVE------
191 ------S--EAHPGSVQIYPVAALE------RIN 189 ------S--EAHPGSVQIYPVAALE------RIN
192 >1ihvA 190 >1ihvA
193 NF-RVYYRDSRDPVWKGPA-KLLWKGEGAV-------VIQDN-------S 191 NF-RVYYRDSRDPVWKGPA-KLLWKGEGAV-------VIQDN-------S
194 DI--------------KVVPRRKAK-----IIRD 192 DI--------------KVVPRRKAK-----IIRD
195 </help> 193 ]]></help>
196 <citations> 194 <citations>
197 <citation type="doi">10.1006/jmbi.2000.4042</citation> 195 <citation type="doi">10.1006/jmbi.2000.4042</citation>
198 </citations> 196 </citations>
199 </tool> 197 </tool>