Mercurial > repos > iuc > mothur_pairwise_seqs

comparison pairwise.seqs.xml @ 2:db466fbe5fa3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:55:43 -0400
parents fe6e11f9f639
children c05906ab8c41
comparison
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1:7addb1047636 2:db466fbe5fa3
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 14
15 echo 'pairwise.seqs( 15 echo 'pairwise.seqs(
16 fasta=fasta.dat, 16 fasta=fasta.dat,
17 align=$align, 17 align=$align,
18 #if $calc: 18 #if $calc:
19 calc=$calc, 19 calc=$calc,
20 #end if 20 #end if
21 $countends 21 $countends
22 #if float($cutoff) > 0.0: 22 #if float($cutoff) > 0.0:
23 cutoff=$cutoff, 23 cutoff=$cutoff,
24 #end if 24 #end if
25 #if $scoring.setby == "user": 25 #if $scoring.setby == "user":
26 match=$scoring.match, 26 match=$scoring.match,
27 mismatch=$scoring.mismatch, 27 mismatch=$scoring.mismatch,
28 gapopen=$scoring.gapopen, 28 gapopen=$scoring.gapopen,
29 gapextend=$scoring.gapextend, 29 gapextend=$scoring.gapextend,
30 #end if 30 #end if
31 #if $output: 31 #if $output:
32 output=$output, 32 output=$output,
33 #end if 33 #end if
34 processors='\${GALAXY_SLOTS:-8}' 34 processors='\${GALAXY_SLOTS:-8}'
35 )' 35 )'
36 | sed 's/ //g' ## mothur trips over whitespace 36 | sed 's/ //g' ## mothur trips over whitespace
37 | mothur 37 | mothur
38 | tee mothur.out.log 38 | tee mothur.out.log
39 ]]></command> 39 ]]></command>
40 <inputs> 40 <inputs>
41 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> 41 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
42 <param name="align" type="select" label="align - Select a pairwise alignment method" help=""> 42 <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
43 <option value="needleman" selected="true">needleman (default)</option> 43 <option value="needleman" selected="true">needleman (default)</option>
68 <param name="output" type="select" label="output - Distance Matrix Output Format" help=""> 68 <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
69 <option value="" selected="true">Column-Formatted Matrix (Default)</option> 69 <option value="" selected="true">Column-Formatted Matrix (Default)</option>
70 <option value="lt">Phylip formatted Lower Triangle Matrix</option> 70 <option value="lt">Phylip formatted Lower Triangle Matrix</option>
71 <option value="square">Phylip formatted Square Matrix</option> 71 <option value="square">Phylip formatted Square Matrix</option>
72 </param> 72 </param>
73 <expand macro="param-savelog"/>
73 </inputs> 74 </inputs>
74 <outputs> 75 <outputs>
75 <expand macro="logfile-output"/> 76 <expand macro="logfile-output"/>
76 <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.dist" label="${tool.name} on ${on_string}: dist"> 77 <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.dist" label="${tool.name} on ${on_string}: dist">
77 <change_format> 78 <change_format>
87 <param name="calc" value=""/> 88 <param name="calc" value=""/>
88 <param name="countends" value=""/> 89 <param name="countends" value=""/>
89 <param name="cutoff" value="0.0"/> 90 <param name="cutoff" value="0.0"/>
90 <param name="setby" value="default"/> 91 <param name="setby" value="default"/>
91 <param name="output" value=""/> 92 <param name="output" value=""/>
93 <param name="savelog" value="true"/>
92 <expand macro="logfile-test"/> 94 <expand macro="logfile-test"/>
93 <output name="out_dist" md5="bb2fefcda217604cd0e985f676168379"/> 95 <output name="out_dist" md5="bb2fefcda217604cd0e985f676168379"/>
94 </test> 96 </test>
95 <test> 97 <test>
96 <param name="fasta" value="amazon.unique.fasta"/> 98 <param name="fasta" value="amazon.unique.fasta"/>
102 <param name="match" value="2"/> 104 <param name="match" value="2"/>
103 <param name="mismatch" value="-1"/> 105 <param name="mismatch" value="-1"/>
104 <param name="gapopen" value="-2"/> 106 <param name="gapopen" value="-2"/>
105 <param name="gapextend" value="-1"/> 107 <param name="gapextend" value="-1"/>
106 <param name="output" value="lt"/> 108 <param name="output" value="lt"/>
109 <param name="savelog" value="true"/>
107 <expand macro="logfile-test"/> 110 <expand macro="logfile-test"/>
108 <output name="out_dist" md5="945c494bee1700c7f9a4ce5d87355190"/> 111 <output name="out_dist" md5="945c494bee1700c7f9a4ce5d87355190"/>
109 </test> 112 </test>
110 </tests> 113 </tests>
111 <help> 114 <help><![CDATA[
112 <![CDATA[
113 115
114 @MOTHUR_OVERVIEW@ 116 @MOTHUR_OVERVIEW@
115 117
116 .. _Mothur: https://www.mothur.org/wiki/Main_Page 118 .. _Mothur: https://www.mothur.org/wiki/Main_Page
117 119
121 123
122 .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix 124 .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix
123 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix 125 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
124 .. _pairwise.seqs: https://www.mothur.org/wiki/Pairwise.seqs 126 .. _pairwise.seqs: https://www.mothur.org/wiki/Pairwise.seqs
125 127
126 ]]> 128 ]]></help>
127 </help>
128 <expand macro="citations"/> 129 <expand macro="citations"/>
129 </tool> 130 </tool>