Mercurial > repos > iuc > mothur_sort_seqs

comparison sort.seqs.xml @ 2:6619e67b064d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:04:32 -0400
parents a8653fd1ca73
children 437838af4988
comparison
equal deleted inserted replaced
1:1f30e0b31b99 2:6619e67b064d
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"/>
58 <param name="name_in" type="data" format="mothur.names" optional="true" label="names - name reference" help="format must be mothur.names"/> 58 <param name="name_in" type="data" format="mothur.names" optional="true" label="names - name reference" help="format must be mothur.names"/>
59 <param name="tax_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - taxonomy reference" help="format must be mothur.seq.taxonomy"/> 59 <param name="tax_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - taxonomy reference" help="format must be mothur.seq.taxonomy"/>
60 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - sort" help="format must be mothur.accnos"/> 60 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - sort" help="format must be mothur.accnos"/>
61 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="format must be mothur.count_table (generated by count.seqs)"/> 61 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="format must be mothur.count_table (generated by count.seqs)"/>
62 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/> 62 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/>
63 <expand macro="param-savelog"/>
63 </inputs> 64 </inputs>
64 <outputs> 65 <outputs>
65 <expand macro="logfile-output"/> 66 <expand macro="logfile-output"/>
66 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.fasta"> 67 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.fasta">
67 <filter>fasta_in</filter> 68 <filter>fasta_in</filter>
84 </outputs> 85 </outputs>
85 <tests> 86 <tests>
86 <test> 87 <test>
87 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> 88 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
88 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> 89 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
90 <param name="savelog" value="true"/>
89 <expand macro="logfile-test"/> 91 <expand macro="logfile-test"/>
90 </test> 92 </test>
91 <test> 93 <test>
92 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> 94 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
93 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/> 95 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
96 <param name="savelog" value="true"/>
94 <expand macro="logfile-test"/> 97 <expand macro="logfile-test"/>
95 </test> 98 </test>
96 <test> 99 <test>
97 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 100 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
98 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> 101 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
102 <param name="savelog" value="true"/>
99 <expand macro="logfile-test"/> 103 <expand macro="logfile-test"/>
100 </test> 104 </test>
101 <test> 105 <test>
102 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> 106 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
103 <param name="count" value="amazon.count_table" ftype="mothur.count_table"/> 107 <param name="count" value="amazon.count_table" ftype="mothur.count_table"/>
104 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> 108 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
109 <param name="savelog" value="true"/>
105 <expand macro="logfile-test"/> 110 <expand macro="logfile-test"/>
106 </test> 111 </test>
107 <test><!-- test with multiple file types input --> 112 <test><!-- test with multiple file types input -->
108 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> 113 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
109 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> 114 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
110 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 115 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
111 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> 116 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
112 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/> 117 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
113 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> 118 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
119 <param name="savelog" value="true"/>
114 <expand macro="logfile-test"/> 120 <expand macro="logfile-test"/>
115 </test> 121 </test>
116 </tests> 122 </tests>
117 <help> 123 <help><![CDATA[
118 <![CDATA[
119 124
120 @MOTHUR_OVERVIEW@ 125 @MOTHUR_OVERVIEW@
121 126
122 **Command Documentation** 127 **Command Documentation**
123 128
124 The sort.seqs_ command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order. 129 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. 130 You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads.
126 131
127 .. _sort.seqs: https://www.mothur.org/wiki/Sort.seqs 132 .. _sort.seqs: https://www.mothur.org/wiki/Sort.seqs
128 133
129 ]]> 134 ]]></help>
130 </help>
131 <expand macro="citations"/> 135 <expand macro="citations"/>
132 </tool> 136 </tool>