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comparison seq.error.xml @ 3:5aa51a579879 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 09:58:46 -0500
parents b85d7c129afb
children 165cd9cb3aff
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2:40d652bcfae1 3:5aa51a579879
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 "$name_in" name_in.dat && 14 ln -s '$name_in' name_in.dat &&
15 ln -s "$count" count.dat && 15 ln -s '$count' count.dat &&
16 ln -s "$alignment.template" alignment.template.dat && 16 ln -s '$alignment.template' alignment.template.dat &&
17 #if $qual.use == "yes": 17 #if $qual.use == "yes":
18 ln -s "$qual.qfile_in" qfile_in.dat && 18 ln -s '$qual.qfile_in' qfile_in.dat &&
19 ln -s "$qual.alignreport_in" alignreport_in.dat && 19 ln -s '$qual.alignreport_in' alignreport_in.dat &&
20 #end if 20 #end if
21 21
22 echo 'seq.error( 22 echo 'seq.error(
23 fasta=fasta_in.dat, 23 fasta=fasta_in.dat,
24 reference=alignment.template.dat, 24 reference=alignment.template.dat,
25 #if $name_in: 25 #if $name_in:
26 name=name_in.dat, 26 name=name_in.dat,
27 #end if 27 #end if
28 #if $qual.use == "yes": 28 #if $qual.use == "yes":
29 qfile=qfile_in.dat, 29 qfile=qfile_in.dat,
30 report=alignreport_in.dat, 30 report=alignreport_in.dat,
31 #end if 31 #end if
32 #if $threshold: 32 #if $threshold:
33 threshold=$threshold, 33 threshold=$threshold,
34 #end if 34 #end if
35 ignorechimeras=$ignorechimeras, 35 ignorechimeras=$ignorechimeras,
36 #if $count: 36 #if $count:
37 count=count.dat, 37 count=count.dat,
38 #end if 38 #end if
39 #if $fasta_in.is_of_type('mothur.align') 39 #if $fasta_in.is_of_type('mothur.align')
40 aligned=T, 40 aligned=T,
41 #else 41 #else
42 aligned=F, 42 aligned=F,
43 #end if 43 #end if
44 processors='\${GALAXY_SLOTS:-8}' 44 processors='\${GALAXY_SLOTS:-8}'
45 )' 45 )'
46 | sed 's/ //g' ## mothur trips over whitespace 46 | sed 's/ //g' ## mothur trips over whitespace
47 | mothur 47 | mothur
48 | tee mothur.out.log 48 | tee mothur.out.log
49 ]]></command> 49 ]]></command>
50 <inputs> 50 <inputs>
51 <param name="fasta_in" type="data" format="mothur.align,fasta" label="fasta - Candidate Sequences" help="sequences must be aligned"/> 51 <param name="fasta_in" type="data" format="mothur.align,fasta" label="fasta - Candidate Sequences" help="sequences must be aligned"/>
52 <conditional name="alignment"> 52 <conditional name="alignment">
53 <param name="source" type="select" label="Select Reference Template from" help=""> 53 <param name="source" type="select" label="Select Reference Template from" help="">
151 <output name="seq_reverse_out" md5="5618b1e431306ec1275f1572d6c0c2fc"/> 151 <output name="seq_reverse_out" md5="5618b1e431306ec1275f1572d6c0c2fc"/>
152 <output name="summary_out" md5="d33bddf9b112f2f3a80b38cf7ac50e6a"/> 152 <output name="summary_out" md5="d33bddf9b112f2f3a80b38cf7ac50e6a"/>
153 <expand macro="logfile-test"/> 153 <expand macro="logfile-test"/>
154 </test> 154 </test>
155 </tests> 155 </tests>
156 <help> 156 <help><![CDATA[
157 <![CDATA[
158 157
159 @MOTHUR_OVERVIEW@ 158 @MOTHUR_OVERVIEW@
160 159
161 **Command Documentation** 160 **Command Documentation**
162 161
164 This is demonstrated in https://www.mothur.org/wiki/Schloss_SOP#Error_analysis 163 This is demonstrated in https://www.mothur.org/wiki/Schloss_SOP#Error_analysis
165 164
166 .. _template_alignment: https://www.mothur.org/wiki/Alignment_database 165 .. _template_alignment: https://www.mothur.org/wiki/Alignment_database
167 .. _seq.error: https://www.mothur.org/wiki/Seq.error 166 .. _seq.error: https://www.mothur.org/wiki/Seq.error
168 167
169 ]]> 168 ]]></help>
170 </help>
171 <expand macro="citations"/> 169 <expand macro="citations"/>
172 </tool> 170 </tool>