Mercurial > repos > iuc > mothur_pcr_seqs

comparison pcr.seqs.xml @ 3:1d43bafb7108 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 09:38:08 -0500
parents 0ef1f460a44f
children 405401e66af4
comparison
equal deleted inserted replaced
2:0c058af8c7cd 3:1d43bafb7108
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 "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 ln -s "$name_in" name_in.dat && 14 ln -s '$name_in' name_in.dat &&
15 ln -s "$group_in" group_in.dat && 15 ln -s '$group_in' group_in.dat &&
16 ln -s "$taxonomy_in" taxonomy_in.dat && 16 ln -s '$taxonomy_in' taxonomy_in.dat &&
17 #if $trim.method == "oligos": 17 #if $trim.method == "oligos":
18 ln -s "$trim.oligos" trim.oligos.dat && 18 ln -s '$trim.oligos' trim.oligos.dat &&
19 #elif $trim.method == "reference": 19 #elif $trim.method == "reference":
20 ln -s "$trim.ecoli" trim.ecoli.dat && 20 ln -s '$trim.ecoli' trim.ecoli.dat &&
21 #end if
22
23 echo 'pcr.seqs(
24 fasta=fasta.dat,
25 #if $name_in
26 name=name_in.dat,
27 #end if
28 #if $group_in:
29 group=group_in.dat,
30 #end if
31 #if $taxonomy_in:
32 taxonomy=taxonomy_in.dat,
33 #end if
34 #if $trim.method == "oligos":
35 oligos=trim.oligos.dat,
36 nomatch=$trim.nomatch,
37 $trim.keepprimer
38 #elif $trim.method == "reference":
39 ecoli=trim.ecoli.dat,
40 #elif $trim.method == "position":
41 start=$trim.start,
42 #if $trim.end and int($trim.end) > 0:
43 end=$trim.end,
21 #end if 44 #end if
22 45 #end if
23 echo 'pcr.seqs( 46 pdiffs=$pdiffs,
24 fasta=fasta.dat, 47 rdiffs=$rdiffs,
25 #if $name_in 48 $keepdots
26 name=name_in.dat, 49 processors='\${GALAXY_SLOTS:-8}'
27 #end if 50 )'
28 #if $group_in: 51 | sed 's/ //g' ## mothur trips over whitespace
29 group=group_in.dat, 52 | mothur
30 #end if 53 | tee mothur.out.log
31 #if $taxonomy_in:
32 taxonomy=taxonomy_in.dat,
33 #end if
34 #if $trim.method == "oligos":
35 oligos=trim.oligos.dat,
36 nomatch=$trim.nomatch,
37 $trim.keepprimer
38 #elif $trim.method == "reference":
39 ecoli=trim.ecoli.dat,
40 #elif $trim.method == "position":
41 start=$trim.start,
42 #if $trim.end and int($trim.end) > 0:
43 end=$trim.end,
44 #end if
45 #end if
46 #if $pdiffs:
47 pdiffs=$pdiffs,
48 #end if
49 $keepdots
50 processors='\${GALAXY_SLOTS:-8}'
51 )'
52 | sed 's/ //g' ## mothur trips over whitespace
53 | mothur
54 | tee mothur.out.log
55 ]]></command> 54 ]]></command>
56 <inputs> 55 <inputs>
57 <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Sequences" help="sequences must be aligned"/> 56 <param name="fasta" type="data" format="mothur.align,fasta" label="fasta - Candiate Sequences" help="sequences must be aligned"/>
58 <conditional name="trim"> 57 <conditional name="trim">
59 <param name="method" type="select" label="Trim with an oligos file?" help=""> 58 <param name="method" type="select" label="Trim with an oligos file?" help="">
60 <option value="oligos">oligos</option> 59 <option value="oligos">oligos</option>
61 <option value="reference">reference sequence</option> 60 <option value="reference">reference sequence</option>
62 <option value="position">start and end positions</option> 61 <option value="position">start and end positions</option>
79 </conditional> 78 </conditional>
80 <param name="keepdots" type="boolean" falsevalue="keepdots=false," truevalue="" checked="true" label="keepdots - keep the leading and trailing alignment dots in the output sequences"/> 79 <param name="keepdots" type="boolean" falsevalue="keepdots=false," truevalue="" checked="true" label="keepdots - keep the leading and trailing alignment dots in the output sequences"/>
81 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Sequence Taxonomy"/> 80 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Sequence Taxonomy"/>
82 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/> 81 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/>
83 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Group file"/> 82 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Group file"/>
84 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/> 83 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the forward primers (default 0)"/>
84 <param name="rdiffs" type="integer" value="0" min="0" label="rdiffs - number of differences to allow in the reverse primers (default 0)"/>
85 </inputs> 85 </inputs>
86 <outputs> 86 <outputs>
87 <expand macro="logfile-output"/> 87 <expand macro="logfile-output"/>
88 <data name="pcr_fasta" format="mothur.align" from_work_dir="fasta.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/> 88 <data name="pcr_fasta" format_source="fasta" from_work_dir="fasta.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/>
89 <data name="scrap_fasta" format="mothur.align" from_work_dir="fasta.scrap.pcr.dat" label="${tool.name} on ${on_string}: pcr.scrap.fasta"/> 89 <data name="scrap_fasta" format_source="fasta" from_work_dir="fasta.scrap.pcr.dat" label="${tool.name} on ${on_string}: pcr.scrap.fasta"/>
90 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pcr.dat" label="${tool.name} on ${on_string}: tax.summary"> 90 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pcr.dat" label="${tool.name} on ${on_string}: tax.summary">
91 <filter>taxonomy_in</filter> 91 <filter>taxonomy_in</filter>
92 </data> 92 </data>
93 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.groups"> 93 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.groups">
94 <filter>group_in</filter> 94 <filter>group_in</filter>
114 </test> 114 </test>
115 <test><!-- test with reference method --> 115 <test><!-- test with reference method -->
116 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> 116 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
117 <param name="keepdots" value="keepdots=false,"/> 117 <param name="keepdots" value="keepdots=false,"/>
118 <param name="method" value="reference"/> 118 <param name="method" value="reference"/>
119 <param name="ecoli" value="amazon.align_head"/> 119 <param name="ecoli" value="amazon.align_head" ftype="mothur.align"/>
120 <param name="name_in" value="amazon.align_head.names"/> 120 <param name="name_in" value="amazon.align_head.names"/>
121 <param name="pdiffs" value="2"/> 121 <param name="pdiffs" value="2"/>
122 <expand macro="logfile-test"/> 122 <expand macro="logfile-test"/>
123 <output name="pcr_fasta" md5="4bef877bd45f47041f3d17dc017f21ea" ftype="mothur.align"/> 123 <output name="pcr_fasta" md5="4bef877bd45f47041f3d17dc017f21ea" ftype="mothur.align"/>
124 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> 124 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
140 <output name="name_out" md5="62eb1162557408509c931496071add85" ftype="mothur.names"/> 140 <output name="name_out" md5="62eb1162557408509c931496071add85" ftype="mothur.names"/>
141 <output name="taxonomy_out" md5="4d72981cefd8b45d4f2793a28dccd9e4" ftype="mothur.seq.taxonomy"/> 141 <output name="taxonomy_out" md5="4d72981cefd8b45d4f2793a28dccd9e4" ftype="mothur.seq.taxonomy"/>
142 <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/> 142 <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/>
143 </test> 143 </test>
144 </tests> 144 </tests>
145 <help> 145 <help><![CDATA[
146 <![CDATA[
147 146
148 @MOTHUR_OVERVIEW@ 147 @MOTHUR_OVERVIEW@
149 148
150 **Command Documentation** 149 **Command Documentation**
151 150
152 The pcr.seqs_ command assigns sequences to chosen taxonomy outline. 151 The pcr.seqs_ command assigns sequences to chosen taxonomy outline.
153 152
154 .. _pcr.seqs: https://www.mothur.org/wiki/Pcr.seqs 153 .. _pcr.seqs: https://www.mothur.org/wiki/Pcr.seqs
155 154
156 ]]> 155 ]]></help>
157 </help>
158 <expand macro="citations"/> 156 <expand macro="citations"/>
159 </tool> 157 </tool>