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comparison t_coffee.xml @ 3:78dd29aa7fc1 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 81a1e79dda127d1afc16c7e456bbec16093a3c3f-dirty
author earlhaminst
date Mon, 20 Feb 2017 06:25:50 -0500
parents df6527887a18
children a91be6005274
comparison
equal deleted inserted replaced
2:df6527887a18 3:78dd29aa7fc1
1 <tool id="t_coffee" name="T-Coffee" version="11.0.8"> 1 <tool id="t_coffee" name="T-Coffee" version="11.0.8_1">
2 <description>multiple sequence alignment</description> 2 <description>multiple sequence alignment</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="11.0.8">t_coffee</requirement> 4 <requirement type="package" version="11.0.8">t_coffee</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
32 32
33 #set $output_opt = '' 33 #set $output_opt = ''
34 #if $outputs 34 #if $outputs
35 #set $outputs_arr = str($outputs).split(',') 35 #set $outputs_arr = str($outputs).split(',')
36 #for $o in $outputs_arr 36 #for $o in $outputs_arr
37 #if $o not in ['cigar', 'dnd'] 37 #if $o != 'dnd'
38 #set $output_opt += $o + ',' 38 #set $output_opt += $o + ','
39 #end if 39 #end if
40 #end for 40 #end for
41 #if 'cigar' in $outputs_arr and 'fasta_aln' not in $outputs_arr
42 #set $output_opt += 'fasta_aln,'
43 #end if
44 #else 41 #else
45 #set $outputs_arr = [] 42 #set $outputs_arr = []
46 #end if 43 #end if
47 #if $output_opt 44 #if $output_opt
48 #set $output_opt = '-output ' + $output_opt[:-1] 45 #set $output_opt = '-output ' + $output_opt[:-1]
49 #end if 46 #end if
50 47
51 t_coffee '$input' $method_opt $output_opt -n_core \${GALAXY_SLOTS:-1} -run_name t_coffee_out -quiet 48 t_coffee '$input' $method_opt $output_opt -n_core \${GALAXY_SLOTS:-1} -run_name t_coffee_out -quiet
52
53 #if 'cigar' in $outputs_arr
54 && python '$__tool_directory__/t_coffee_to_cigar.py' t_coffee_out.fasta_aln > '$cigar'
55 #end if
56 ]]> 49 ]]>
57 </command> 50 </command>
58 <inputs> 51 <inputs>
59 <conditional name="input_type"> 52 <conditional name="input_type">
60 <param name="filter_fasta" type="select" label="Filter FASTA input?"> 53 <param name="filter_fasta" type="select" label="Filter FASTA input?">
91 <option value="lalign_id_pair">lalign_id_pair</option> 84 <option value="lalign_id_pair">lalign_id_pair</option>
92 <option value="slow_pair">slow_pair</option> 85 <option value="slow_pair">slow_pair</option>
93 <option value="proba_pair">proba_pair</option> 86 <option value="proba_pair">proba_pair</option>
94 </param> 87 </param>
95 <param name="outputs" type="select" multiple="true" optional="false" display="checkboxes" label="Output formats"> 88 <param name="outputs" type="select" multiple="true" optional="false" display="checkboxes" label="Output formats">
96 <option value="cigar">CIGAR</option>
97 <option value="clustalw_aln">clustalw_aln</option> 89 <option value="clustalw_aln">clustalw_aln</option>
98 <option value="dnd" selected="true">dnd</option> 90 <option value="dnd" selected="true">dnd</option>
99 <option value="fasta_aln">fasta_aln</option> 91 <option value="fasta_aln">fasta_aln</option>
100 <option value="fasta_seq">fasta_seq</option> 92 <option value="fasta_seq">fasta_seq</option>
101 <option value="msf_aln">msf_aln</option> 93 <option value="msf_aln">msf_aln</option>
105 <option value="score_ascii">score_ascii</option> 97 <option value="score_ascii">score_ascii</option>
106 <option value="score_html">score_html</option> 98 <option value="score_html">score_html</option>
107 </param> 99 </param>
108 </inputs> 100 </inputs>
109 <outputs> 101 <outputs>
110 <data name="cigar" format="tabular" label="${tool.name} on ${on_string}: cigar" >
111 <filter>'cigar' in outputs</filter>
112 </data>
113 <data name="clustalw_aln" format="clustalw" label="${tool.name} on ${on_string}: clustalw_aln" from_work_dir="t_coffee_out.clustalw_aln"> 102 <data name="clustalw_aln" format="clustalw" label="${tool.name} on ${on_string}: clustalw_aln" from_work_dir="t_coffee_out.clustalw_aln">
114 <filter>'clustalw_aln' in outputs</filter> 103 <filter>'clustalw_aln' in outputs</filter>
115 </data> 104 </data>
116 <data name="dnd" format="nhx" label="${tool.name} on ${on_string}: newick.dnd" from_work_dir="t_coffee_out.dnd"> 105 <data name="dnd" format="nhx" label="${tool.name} on ${on_string}: newick.dnd" from_work_dir="t_coffee_out.dnd">
117 <filter>'dnd' in outputs</filter> 106 <filter>'dnd' in outputs</filter>
145 <test> 134 <test>
146 <param name="filter_fasta" value="no" /> 135 <param name="filter_fasta" value="no" />
147 <param name="input" value="input.fasta" ftype="fasta" /> 136 <param name="input" value="input.fasta" ftype="fasta" />
148 <param name="method02" value="clustalw_msa" /> 137 <param name="method02" value="clustalw_msa" />
149 <param name="outputs" value="fasta_aln" /> 138 <param name="outputs" value="fasta_aln" />
150 <output name="fasta_aln" file="output1.fasta" /> 139 <output name="fasta_aln" file="output1.fasta" ftype="fasta" />
151 </test> 140 </test>
152 <test> 141 <test>
153 <param name="filter_fasta" value="yes" /> 142 <param name="filter_fasta" value="yes" />
154 <param name="fasta_input" value="input.fasta" ftype="fasta" /> 143 <param name="fasta_input" value="input.fasta" ftype="fasta" />
155 <param name="identifiers" value="ids.txt" ftype="txt" /> 144 <param name="identifiers" value="ids.txt" ftype="txt" />
156 <param name="method02" value="clustalw_msa" /> 145 <param name="method02" value="clustalw_msa" />
157 <param name="outputs" value="cigar" /> 146 <param name="outputs" value="fasta_aln" />
158 <output name="cigar" file="cigar.tabular" /> 147 <output name="fasta_aln" file="output2.fasta" ftype="fasta" />
159 </test> 148 </test>
160 </tests> 149 </tests>
161 <help> 150 <help>
162 **What it does** 151 **What it does**
163 152