Mercurial > repos > iuc > mothur_pcr_seqs

comparison pcr.seqs.xml @ 0:692381e1abfe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:58:12 -0400
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children 9a1fd25e2a1a
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-1:000000000000 0:692381e1abfe
1 <tool profile="16.07" id="mothur_pcr_seqs" name="Pcr.seqs" version="@WRAPPER_VERSION@.0">
2 <description>Trim sequences</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat &&
14 ln -s "$name_in" name_in.dat &&
15 ln -s "$group_in" group_in.dat &&
16 ln -s "$taxonomy_in" taxonomy_in.dat &&
17 #if $trim.method == "oligos":
18 ln -s "$trim.oligos" trim.oligos.dat &&
19 #elif $trim.method == "reference":
20 ln -s "$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,
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>
56 <inputs>
57 <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Sequences" help="sequences must be aligned"/>
58 <conditional name="trim">
59 <param name="method" type="select" label="Trim with an oligos file?" help="">
60 <option value="oligos">oligos</option>
61 <option value="reference">reference sequence</option>
62 <option value="position">start and end positions</option>
63 </param>
64 <when value="oligos">
65 <param name="oligos" type="data" format="mothur.oligos" optional="true" label="oligos - barcodes and primers" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file."/>
66 <param name="nomatch" type="select" label="nomatch - action when no primer is found">
67 <option value="reject" selected="true">reject (default)</option>
68 <option value="keep">keep</option>
69 </param>
70 <param name="keepprimer" type="boolean" falsevalue="" truevalue="keepprimer=true," checked="false" label="keepprimer - keep the primer in the output sequence"/>
71 </when>
72 <when value="reference">
73 <param name="ecoli" type="data" format="mothur.align" optional="true" label="ecoli - An aligned reference sequence for trimming" help="The ecoli parameter is used to provide a fasta file containing a single reference sequence (e.g. for e. coli) this must be aligned. Mothur will trim to the start and end positions of the reference sequence."/>
74 </when>
75 <when value="position">
76 <param name="start" type="integer" min="0" value="0" optional="true" label="start - a starting position to trim to"/>
77 <param name="end" type="integer" value="" optional="true" min="0" label="end - a ending position to trim from"/>
78 </when>
79 </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"/>
81 <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"/>
83 <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)"/>
85 </inputs>
86 <outputs>
87 <expand macro="logfile-output"/>
88 <data name="pcr_fasta" format="mothur.align" from_work_dir="fasta.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/>
89 <data name="scrap_fasta" format="mothur.align" from_work_dir="fasta.scrap.pcr.dat" label="${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 ${on_string}: tax.summary">
91 <filter>taxonomy_in</filter>
92 </data>
93 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.groups">
94 <filter>group_in</filter>
95 </data>
96 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.names">
97 <filter>name_in</filter>
98 </data>
99 <data name="accnos_out" format="mothur.accnos" from_work_dir="fasta*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos">
100 <filter>trim['method'] =='oligos'</filter>
101 </data>
102 </outputs>
103 <tests>
104 <test><!-- test with position method -->
105 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
106 <param name="keepdots" value=""/>
107 <param name="method" value="position"/>
108 <param name="start" value="0"/>
109 <param name="end" value="0"/>
110 <param name="pdiffs" value="0"/>
111 <expand macro="logfile-test"/>
112 <output name="pcr_fasta" md5="4f9c3a835bbba51c64fbf86c8a467d0e" ftype="mothur.align"/>
113 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
114 </test>
115 <test><!-- test with reference method -->
116 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
117 <param name="keepdots" value="keepdots=false,"/>
118 <param name="method" value="reference"/>
119 <param name="ecoli" value="amazon.align_head"/>
120 <param name="name_in" value="amazon.align_head.names"/>
121 <param name="pdiffs" value="2"/>
122 <expand macro="logfile-test"/>
123 <output name="pcr_fasta" md5="4bef877bd45f47041f3d17dc017f21ea" ftype="mothur.align"/>
124 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
125 <output name="name_out" md5="0c58174137c2ecabf7da9ab492ea46fc" ftype="mothur.names"/>
126 </test>
127 <test><!-- test with oligos and all outputs -->
128 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
129 <param name="method" value="oligos"/>
130 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
131 <param name="name_in" value="amazon.names" ftype="mothur.names"/>
132 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
133 <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
134 <param name="start" value="5"/>
135 <param name="end" value="50"/>
136 <expand macro="logfile-test"/>
137 <output name="pcr_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
138 <output name="scrap_fasta" md5="0b63807f339dfd88cf958f7b069eba02" ftype="mothur.align"/>
139 <output name="group_out" md5="301c358e61d38c83cc7382a8a210089a" ftype="mothur.groups"/>
140 <output name="name_out" md5="62eb1162557408509c931496071add85" ftype="mothur.names"/>
141 <output name="taxonomy_out" md5="4d72981cefd8b45d4f2793a28dccd9e4" ftype="mothur.seq.taxonomy"/>
142 <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/>
143 </test>
144 </tests>
145 <help>
146 <![CDATA[
147
148 @MOTHUR_OVERVIEW@
149
150 **Command Documentation**
151
152 The pcr.seqs_ command assigns sequences to chosen taxonomy outline.
153
154 .. _pcr.seqs: https://www.mothur.org/wiki/Pcr.seqs
155
156 ]]>
157 </help>
158 <expand macro="citations"/>
159 </tool>