Mercurial > repos > iuc > mothur_pcr_seqs

comparison pcr.seqs.xml @ 2:9a1fd25e2a1a 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 22:19:52 -0400
parents 692381e1abfe
children 644d8a3af62d
comparison
equal deleted inserted replaced
1:d2e1ae25974c 2:9a1fd25e2a1a
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 <expand macro="param-savelog"/>
85 </inputs> 86 </inputs>
86 <outputs> 87 <outputs>
87 <expand macro="logfile-output"/> 88 <expand macro="logfile-output"/>
88 <data name="pcr_fasta" format="mothur.align" from_work_dir="fasta.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/> 89 <data name="pcr_fasta" format_source="fasta" from_work_dir="fasta.pcr.dat" label="${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 ${on_string}: pcr.scrap.fasta"/> 90 <data name="scrap_fasta" format_source="fasta" from_work_dir="fasta.scrap.pcr.dat" label="${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 ${on_string}: tax.summary"> 91 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pcr.dat" label="${tool.name} on ${on_string}: tax.summary">
91 <filter>taxonomy_in</filter> 92 <filter>taxonomy_in</filter>
92 </data> 93 </data>
93 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.groups"> 94 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.groups">
94 <filter>group_in</filter> 95 <filter>group_in</filter>
106 <param name="keepdots" value=""/> 107 <param name="keepdots" value=""/>
107 <param name="method" value="position"/> 108 <param name="method" value="position"/>
108 <param name="start" value="0"/> 109 <param name="start" value="0"/>
109 <param name="end" value="0"/> 110 <param name="end" value="0"/>
110 <param name="pdiffs" value="0"/> 111 <param name="pdiffs" value="0"/>
112 <param name="savelog" value="true"/>
111 <expand macro="logfile-test"/> 113 <expand macro="logfile-test"/>
112 <output name="pcr_fasta" md5="4f9c3a835bbba51c64fbf86c8a467d0e" ftype="mothur.align"/> 114 <output name="pcr_fasta" md5="4f9c3a835bbba51c64fbf86c8a467d0e" ftype="mothur.align"/>
113 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> 115 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
114 </test> 116 </test>
115 <test><!-- test with reference method --> 117 <test><!-- test with reference method -->
116 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> 118 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
117 <param name="keepdots" value="keepdots=false,"/> 119 <param name="keepdots" value="keepdots=false,"/>
118 <param name="method" value="reference"/> 120 <param name="method" value="reference"/>
119 <param name="ecoli" value="amazon.align_head"/> 121 <param name="ecoli" value="amazon.align_head" ftype="mothur.align"/>
120 <param name="name_in" value="amazon.align_head.names"/> 122 <param name="name_in" value="amazon.align_head.names"/>
121 <param name="pdiffs" value="2"/> 123 <param name="pdiffs" value="2"/>
124 <param name="savelog" value="true"/>
122 <expand macro="logfile-test"/> 125 <expand macro="logfile-test"/>
123 <output name="pcr_fasta" md5="4bef877bd45f47041f3d17dc017f21ea" ftype="mothur.align"/> 126 <output name="pcr_fasta" md5="4bef877bd45f47041f3d17dc017f21ea" ftype="mothur.align"/>
124 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> 127 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
125 <output name="name_out" md5="0c58174137c2ecabf7da9ab492ea46fc" ftype="mothur.names"/> 128 <output name="name_out" md5="0c58174137c2ecabf7da9ab492ea46fc" ftype="mothur.names"/>
126 </test> 129 </test>
131 <param name="name_in" value="amazon.names" ftype="mothur.names"/> 134 <param name="name_in" value="amazon.names" ftype="mothur.names"/>
132 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 135 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
133 <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 136 <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
134 <param name="start" value="5"/> 137 <param name="start" value="5"/>
135 <param name="end" value="50"/> 138 <param name="end" value="50"/>
139 <param name="savelog" value="true"/>
136 <expand macro="logfile-test"/> 140 <expand macro="logfile-test"/>
137 <output name="pcr_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> 141 <output name="pcr_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
138 <output name="scrap_fasta" md5="0b63807f339dfd88cf958f7b069eba02" ftype="mothur.align"/> 142 <output name="scrap_fasta" md5="0b63807f339dfd88cf958f7b069eba02" ftype="mothur.align"/>
139 <output name="group_out" md5="301c358e61d38c83cc7382a8a210089a" ftype="mothur.groups"/> 143 <output name="group_out" md5="301c358e61d38c83cc7382a8a210089a" ftype="mothur.groups"/>
140 <output name="name_out" md5="62eb1162557408509c931496071add85" ftype="mothur.names"/> 144 <output name="name_out" md5="62eb1162557408509c931496071add85" ftype="mothur.names"/>
141 <output name="taxonomy_out" md5="4d72981cefd8b45d4f2793a28dccd9e4" ftype="mothur.seq.taxonomy"/> 145 <output name="taxonomy_out" md5="4d72981cefd8b45d4f2793a28dccd9e4" ftype="mothur.seq.taxonomy"/>
142 <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/> 146 <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/>
143 </test> 147 </test>
144 </tests> 148 </tests>
145 <help> 149 <help><![CDATA[
146 <![CDATA[
147 150
148 @MOTHUR_OVERVIEW@ 151 @MOTHUR_OVERVIEW@
149 152
150 **Command Documentation** 153 **Command Documentation**
151 154
152 The pcr.seqs_ command assigns sequences to chosen taxonomy outline. 155 The pcr.seqs_ command assigns sequences to chosen taxonomy outline.
153 156
154 .. _pcr.seqs: https://www.mothur.org/wiki/Pcr.seqs 157 .. _pcr.seqs: https://www.mothur.org/wiki/Pcr.seqs
155 158
156 ]]> 159 ]]></help>
157 </help>
158 <expand macro="citations"/> 160 <expand macro="citations"/>
159 </tool> 161 </tool>