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comparison seq.error.xml @ 2:a5418319c97a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:06:03 -0400
parents 45af9683de29
children a03c9ebf1959
comparison
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1:29fa3670faa5 2:a5418319c97a
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="">
76 <when value="no"/> 76 <when value="no"/>
77 </conditional> 77 </conditional>
78 <param name="count" type="data" format="mothur.count_table" optional="true" label="count table"/> 78 <param name="count" type="data" format="mothur.count_table" optional="true" label="count table"/>
79 <param name="threshold" type="float" value="" min="0" max="1" optional="true" label="threshold - error rate at which to report (default 1.)"/> 79 <param name="threshold" type="float" value="" min="0" max="1" optional="true" label="threshold - error rate at which to report (default 1.)"/>
80 <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/> 80 <param name="ignorechimeras" type="boolean" truevalue="true" falsevalue="false" checked="true" label="ignorechimeras - "/>
81 <expand macro="param-savelog"/>
81 </inputs> 82 </inputs>
82 <outputs> 83 <outputs>
83 <expand macro="logfile-output"/> 84 <expand macro="logfile-output"/>
84 <data name="summary_out" format="tabular" from_work_dir="fasta_in*.error.summary" label="${tool.name} on ${on_string}: error.summary"> 85 <data name="summary_out" format="tabular" from_work_dir="fasta_in*.error.summary" label="${tool.name} on ${on_string}: error.summary">
85 <filter>'summary' in output_sel</filter> 86 <filter>'summary' in output_sel</filter>
127 <output name="ref_query_out" md5="42b42eb4c6bc2705ded2c697a757106f"/> 128 <output name="ref_query_out" md5="42b42eb4c6bc2705ded2c697a757106f"/>
128 <output name="seq_out" md5="5a884846a8d94b8482c2935d2e7e43e6"/> 129 <output name="seq_out" md5="5a884846a8d94b8482c2935d2e7e43e6"/>
129 <output name="seq_forward_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/> 130 <output name="seq_forward_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
130 <output name="seq_reverse_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/> 131 <output name="seq_reverse_out" md5="92a24ef3155bc050ae4fd31bab43cf92"/>
131 <output name="summary_out" md5="04abbbd6aa82f084e4a3bd51c4ce98e6"/> 132 <output name="summary_out" md5="04abbbd6aa82f084e4a3bd51c4ce98e6"/>
133 <param name="savelog" value="true"/>
132 <expand macro="logfile-test"/> 134 <expand macro="logfile-test"/>
133 </test> 135 </test>
134 <test><!--test with qual file and all outputs --> 136 <test><!--test with qual file and all outputs -->
135 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/> 137 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
136 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/> 138 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
148 <output name="qual_reverse_out" md5="81f17617ba99cac5807e454a626eb006"/> 150 <output name="qual_reverse_out" md5="81f17617ba99cac5807e454a626eb006"/>
149 <output name="seq_out" md5="69a8ec131df0b1d4d95eaeb04e057941"/> 151 <output name="seq_out" md5="69a8ec131df0b1d4d95eaeb04e057941"/>
150 <output name="seq_forward_out" md5="dbcbbefdc83c2a7c045e3930850cdbd9"/> 152 <output name="seq_forward_out" md5="dbcbbefdc83c2a7c045e3930850cdbd9"/>
151 <output name="seq_reverse_out" md5="5618b1e431306ec1275f1572d6c0c2fc"/> 153 <output name="seq_reverse_out" md5="5618b1e431306ec1275f1572d6c0c2fc"/>
152 <output name="summary_out" md5="d33bddf9b112f2f3a80b38cf7ac50e6a"/> 154 <output name="summary_out" md5="d33bddf9b112f2f3a80b38cf7ac50e6a"/>
155 <param name="savelog" value="true"/>
153 <expand macro="logfile-test"/> 156 <expand macro="logfile-test"/>
154 </test> 157 </test>
155 </tests> 158 </tests>
156 <help> 159 <help><![CDATA[
157 <![CDATA[
158 160
159 @MOTHUR_OVERVIEW@ 161 @MOTHUR_OVERVIEW@
160 162
161 **Command Documentation** 163 **Command Documentation**
162 164
164 This is demonstrated in https://www.mothur.org/wiki/Schloss_SOP#Error_analysis 166 This is demonstrated in https://www.mothur.org/wiki/Schloss_SOP#Error_analysis
165 167
166 .. _template_alignment: https://www.mothur.org/wiki/Alignment_database 168 .. _template_alignment: https://www.mothur.org/wiki/Alignment_database
167 .. _seq.error: https://www.mothur.org/wiki/Seq.error 169 .. _seq.error: https://www.mothur.org/wiki/Seq.error
168 170
169 ]]> 171 ]]></help>
170 </help>
171 <expand macro="citations"/> 172 <expand macro="citations"/>
172 </tool> 173 </tool>