Mercurial > repos > iuc > mothur_pairwise_seqs

comparison pairwise.seqs.xml @ 3:cc74f42d74a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:29:51 -0500
parents 4f382764768a
children 74461a54c0cf
comparison
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2:a61942809333 3:cc74f42d74a2
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>
106 <param name="output" value="lt"/> 106 <param name="output" value="lt"/>
107 <expand macro="logfile-test"/> 107 <expand macro="logfile-test"/>
108 <output name="out_dist" md5="945c494bee1700c7f9a4ce5d87355190"/> 108 <output name="out_dist" md5="945c494bee1700c7f9a4ce5d87355190"/>
109 </test> 109 </test>
110 </tests> 110 </tests>
111 <help> 111 <help><![CDATA[
112 <![CDATA[
113 112
114 @MOTHUR_OVERVIEW@ 113 @MOTHUR_OVERVIEW@
115 114
116 .. _Mothur: https://www.mothur.org/wiki/Main_Page 115 .. _Mothur: https://www.mothur.org/wiki/Main_Page
117 116
121 120
122 .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix 121 .. _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 122 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
124 .. _pairwise.seqs: https://www.mothur.org/wiki/Pairwise.seqs 123 .. _pairwise.seqs: https://www.mothur.org/wiki/Pairwise.seqs
125 124
126 ]]> 125 ]]></help>
127 </help>
128 <expand macro="citations"/> 126 <expand macro="citations"/>
129 </tool> 127 </tool>