Mercurial > repos > iuc > mothur_sort_seqs

comparison sort.seqs.xml @ 3:af77b7eda3ce 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 09:20:25 -0500
parents 9900cd702dcf
children 805e64a3ef00
comparison
equal deleted inserted replaced
2:0508c6389434 3:af77b7eda3ce
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 "$fasta_in" fasta_in.dat && 13 ln -s '$fasta_in' fasta_in.dat &&
14 ln -s "$qfile_in" qfile_in.dat && 14 ln -s '$qfile_in' qfile_in.dat &&
15 ln -s "$flow_in" flow_in.dat && 15 ln -s '$flow_in' flow_in.dat &&
16 ln -s "$name_in" name_in.dat && 16 ln -s '$name_in' name_in.dat &&
17 ln -s "$group_in" group_in.dat && 17 ln -s '$group_in' group_in.dat &&
18 ln -s "$tax_in" tax_in.dat && 18 ln -s '$tax_in' tax_in.dat &&
19 ln -s "$accnos" accnos.dat && 19 ln -s '$accnos' accnos.dat &&
20 ln -s "$count" count.dat && 20 ln -s '$count' count.dat &&
21 21
22 echo 'sort.seqs( 22 echo 'sort.seqs(
23 #if $fasta_in: 23 #if $fasta_in:
24 fasta=fasta_in.dat, 24 fasta=fasta_in.dat,
25 #end if 25 #end if
26 #if $qfile_in: 26 #if $qfile_in:
27 qfile=qfile_in.dat, 27 qfile=qfile_in.dat,
28 #end if 28 #end if
29 #if $flow_in: 29 #if $flow_in:
30 flow=flow_in.dat, 30 flow=flow_in.dat,
31 #end if 31 #end if
32 #if $name_in: 32 #if $name_in:
33 name=name_in.dat, 33 name=name_in.dat,
34 #end if 34 #end if
35 #if $group_in: 35 #if $group_in:
36 group=group_in.dat, 36 group=group_in.dat,
37 #end if 37 #end if
38 #if $tax_in: 38 #if $tax_in:
39 taxonomy=tax_in.dat, 39 taxonomy=tax_in.dat,
40 #end if 40 #end if
41 #if $accnos: 41 #if $accnos:
42 accnos=accnos.dat, 42 accnos=accnos.dat,
43 #end if 43 #end if
44 #if $count: 44 #if $count:
45 count=count.dat, 45 count=count.dat,
46 #end if 46 #end if
47 large=$large 47 large=$large
48 )' 48 )'
49 | sed 's/ //g' ## mothur trips over whitespace 49 | sed 's/ //g' ## mothur trips over whitespace
50 | mothur 50 | mothur
51 | tee mothur.out.log 51 | tee mothur.out.log
52 ]]></command> 52 ]]></command>
53 <inputs> 53 <inputs>
54 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences" help="format must be fasta"/> 54 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences" help="format must be fasta"/>
55 <param name="qfile_in" type="data" format="qual454" optional="true" label="qfile - sequence quality" help="format must be qual454"/> 55 <param name="qfile_in" type="data" format="qual454" optional="true" label="qfile - sequence quality" help="format must be qual454"/>
56 <param name="flow_in" type="data" format="mothur.sff.flow" optional="true" label="flow - sff flowgram" help="format must be mothur.sff.flow"/> 56 <param name="flow_in" type="data" format="mothur.sff.flow" optional="true" label="flow - sff flowgram" help="format must be mothur.sff.flow"/>
112 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/> 112 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
113 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> 113 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
114 <expand macro="logfile-test"/> 114 <expand macro="logfile-test"/>
115 </test> 115 </test>
116 </tests> 116 </tests>
117 <help> 117 <help><![CDATA[
118 <![CDATA[
119 118
120 @MOTHUR_OVERVIEW@ 119 @MOTHUR_OVERVIEW@
121 120
122 **Command Documentation** 121 **Command Documentation**
123 122
124 The sort.seqs_ command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order. 123 The sort.seqs_ command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order.
125 You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads. 124 You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads.
126 125
127 .. _sort.seqs: https://www.mothur.org/wiki/Sort.seqs 126 .. _sort.seqs: https://www.mothur.org/wiki/Sort.seqs
128 127
129 ]]> 128 ]]></help>
130 </help>
131 <expand macro="citations"/> 129 <expand macro="citations"/>
132 </tool> 130 </tool>