Mercurial > repos > iuc > mothur_get_seqs

comparison get.seqs.xml @ 3:ef6de2793ab6 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 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:21:22 -0500
parents fa04cbc39523
children 130711597b24
comparison
equal deleted inserted replaced
2:3377284566a0 3:ef6de2793ab6
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 "$accnos" accnos.dat && 13 ln -s '$accnos' accnos.dat &&
14 ln -s "$fasta_in" fasta_in.dat && 14 ln -s '$fasta_in' fasta_in.dat &&
15 ln -s "$fastq_in" fastq_in.dat && 15 ln -s '$fastq_in' fastq_in.dat &&
16 ln -s "$count_in" count_in.dat && 16 ln -s '$count_in' count_in.dat &&
17 ln -s "$qfile_in" qfile_in.dat && 17 ln -s '$qfile_in' qfile_in.dat &&
18 ln -s "$name_in" name_in.dat && 18 ln -s '$name_in' name_in.dat &&
19 ln -s "$group_in" group_in.dat && 19 ln -s '$group_in' group_in.dat &&
20 ln -s "$alignreport_in" alignreport_in.dat && 20 ln -s '$alignreport_in' alignreport_in.dat &&
21 ln -s "$list_in" list_in.dat && 21 ln -s '$list_in' list_in.dat &&
22 ln -s "$taxonomy_in" taxonomy_in.dat && 22 ln -s '$taxonomy_in' taxonomy_in.dat &&
23 23
24 echo 'get.seqs( 24 echo 'get.seqs(
25 accnos=accnos.dat, 25 accnos=accnos.dat,
26 #if $fasta_in: 26 #if $fasta_in:
27 fasta=fasta_in.dat, 27 fasta=fasta_in.dat,
28 #end if 28 #end if
29 #if $fastq_in: 29 #if $fastq_in:
30 fastq=fastq_in.dat, 30 fastq=fastq_in.dat,
31 #end if 31 #end if
32 #if $count_in: 32 #if $count_in:
33 count=count_in.dat, 33 count=count_in.dat,
34 #end if 34 #end if
35 #if $qfile_in: 35 #if $qfile_in:
36 qfile=qfile_in.dat, 36 qfile=qfile_in.dat,
37 #end if 37 #end if
38 #if $name_in: 38 #if $name_in:
39 name=name_in.dat, 39 name=name_in.dat,
40 #end if 40 #end if
41 #if $group_in: 41 #if $group_in:
42 group=group_in.dat, 42 group=group_in.dat,
43 #end if 43 #end if
44 #if $alignreport_in: 44 #if $alignreport_in:
45 alignreport=alignreport_in.dat, 45 alignreport=alignreport_in.dat,
46 #end if 46 #end if
47 #if $list_in: 47 #if $list_in:
48 list=list_in.dat, 48 list=list_in.dat,
49 #end if 49 #end if
50 #if $taxonomy_in: 50 #if $taxonomy_in:
51 taxonomy=taxonomy_in.dat, 51 taxonomy=taxonomy_in.dat,
52 #end if 52 #end if
53 dups=$dups 53 dups=$dups
54 )' 54 )'
55 | sed 's/ //g' ## mothur trips over whitespace 55 | sed 's/ //g' ## mothur trips over whitespace
56 | mothur 56 | mothur
57 | tee mothur.out.log 57 | tee mothur.out.log
58 ]]></command> 58 ]]></command>
59 <inputs> 59 <inputs>
60 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/> 60 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/>
61 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> 61 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
62 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/> 62 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
108 <expand macro="logfile-test"/> 108 <expand macro="logfile-test"/>
109 </test> 109 </test>
110 <test> 110 <test>
111 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> 111 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
112 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> 112 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
113 <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/> 113 <output name="fastq_out" md5="81d026f969e15b8c8701f8dc5f3a6904"/>
114 <expand macro="logfile-test"/> 114 <expand macro="logfile-test"/>
115 </test> 115 </test>
116 <test> 116 <test>
117 <!-- test two input files --> 117 <!-- test two input files -->
118 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> 118 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
119 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> 119 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
120 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> 120 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
121 <param name="dups" value="false"/> 121 <param name="dups" value="false"/>
122 <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/> 122 <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/>
123 <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/> 123 <output name="fastq_out" md5="81d026f969e15b8c8701f8dc5f3a6904"/>
124 <expand macro="logfile-test"/> 124 <expand macro="logfile-test"/>
125 </test> 125 </test>
126 <test> 126 <test>
127 <param name="accnos" value="amazon.bad.accnos"/> 127 <param name="accnos" value="amazon.bad.accnos"/>
128 <param name="count_in" value="amazon.count_table"/> 128 <param name="count_in" value="amazon.count_table"/>
129 <output name="count_out" md5="6892dd99850ce9e9f8f15e77b28f57e2"/> 129 <output name="count_out" md5="6892dd99850ce9e9f8f15e77b28f57e2"/>
130 <expand macro="logfile-test"/> 130 <expand macro="logfile-test"/>
131 </test> 131 </test>
132 </tests> 132 </tests>
133 <help> 133 <help><![CDATA[
134 <![CDATA[
135 134
136 @MOTHUR_OVERVIEW@ 135 @MOTHUR_OVERVIEW@
137 136
138 **Command Documentation** 137 **Command Documentation**
139 138
146 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline 145 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
147 .. _list.seqs: https://www.mothur.org/wiki/list.seqs 146 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
148 .. _get.seqs: https://www.mothur.org/wiki/Get.seqs 147 .. _get.seqs: https://www.mothur.org/wiki/Get.seqs
149 148
150 v.1.27.0 : Updated to Mothur 1.33, added count and fastq params 149 v.1.27.0 : Updated to Mothur 1.33, added count and fastq params
151 ]]> 150
152 </help> 151 ]]></help>
153 <expand macro="citations"/> 152 <expand macro="citations"/>
154 </tool> 153 </tool>