Mercurial > repos > iuc > mothur_pcr_seqs

comparison pcr.seqs.xml @ 1:0ef1f460a44f 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 05:26:29 -0400
parents 3a534aab3952
children 1d43bafb7108
comparison
equal deleted inserted replaced
0:3a534aab3952 1:0ef1f460a44f
2 <description>Trim sequences</description> 2 <description>Trim sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$fasta" fasta.dat && 13 ln -s "$fasta" fasta.dat &&
11 ln -s "$name_in" name_in.dat && 14 ln -s "$name_in" name_in.dat &&
12 ln -s "$group_in" group_in.dat && 15 ln -s "$group_in" group_in.dat &&
13 ln -s "$taxonomy_in" taxonomy_in.dat && 16 ln -s "$taxonomy_in" taxonomy_in.dat &&
46 $keepdots 49 $keepdots
47 processors='\${GALAXY_SLOTS:-8}' 50 processors='\${GALAXY_SLOTS:-8}'
48 )' 51 )'
49 | sed 's/ //g' ## mothur trips over whitespace 52 | sed 's/ //g' ## mothur trips over whitespace
50 | mothur 53 | mothur
54 | tee mothur.out.log
51 ]]></command> 55 ]]></command>
52 <inputs> 56 <inputs>
53 <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Sequences" help="sequences must be aligned"/> 57 <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Sequences" help="sequences must be aligned"/>
54 <conditional name="trim"> 58 <conditional name="trim">
55 <param name="method" type="select" label="Trim with an oligos file?" help=""> 59 <param name="method" type="select" label="Trim with an oligos file?" help="">
79 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Group file"/> 83 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Group file"/>
80 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/> 84 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
81 </inputs> 85 </inputs>
82 <outputs> 86 <outputs>
83 <expand macro="logfile-output"/> 87 <expand macro="logfile-output"/>
84 <data name="pcr_fasta" format="mothur.align" from_work_dir="fasta*.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/> 88 <data name="pcr_fasta" format="mothur.align" from_work_dir="fasta.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/>
85 <data name="scrap_fasta" format="mothur.align" from_work_dir="fasta*.scrap.pcr.dat" label="${tool.name} on ${on_string}: pcr.scrap.fasta"/> 89 <data name="scrap_fasta" format="mothur.align" from_work_dir="fasta.scrap.pcr.dat" label="${tool.name} on ${on_string}: pcr.scrap.fasta"/>
86 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pcr.dat" label="${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 ${on_string}: tax.summary">
87 <filter>taxonomy_in</filter> 91 <filter>taxonomy_in</filter>
88 </data> 92 </data>
89 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pcr.dat" label="${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">
90 <filter>group_in</filter> 94 <filter>group_in</filter>
103 <param name="method" value="position"/> 107 <param name="method" value="position"/>
104 <param name="start" value="0"/> 108 <param name="start" value="0"/>
105 <param name="end" value="0"/> 109 <param name="end" value="0"/>
106 <param name="pdiffs" value="0"/> 110 <param name="pdiffs" value="0"/>
107 <expand macro="logfile-test"/> 111 <expand macro="logfile-test"/>
108 <ouptut name="pcr_fasta" md5="1e78af5a460572e22ce199e522a70388" ftype="mothur.align"/> 112 <output name="pcr_fasta" md5="4f9c3a835bbba51c64fbf86c8a467d0e" ftype="mothur.align"/>
109 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> 113 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
110 </test> 114 </test>
111 <test><!-- test with reference method --> 115 <test><!-- test with reference method -->
112 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> 116 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
113 <param name="keepdots" value="keepdots=false,"/> 117 <param name="keepdots" value="keepdots=false,"/>
114 <param name="method" value="reference"/> 118 <param name="method" value="reference"/>
115 <param name="ecoli" value="amazon.align_head"/> 119 <param name="ecoli" value="amazon.align_head"/>
116 <param name="name_in" value="amazon.align_head.names"/> 120 <param name="name_in" value="amazon.align_head.names"/>
117 <param name="pdiffs" value="2"/> 121 <param name="pdiffs" value="2"/>
118 <expand macro="logfile-test"/> 122 <expand macro="logfile-test"/>
119 <ouptut name="pcr_fasta" md5="1e78af5a460572e22ce199e522a70388" ftype="mothur.align"/> 123 <output name="pcr_fasta" md5="4bef877bd45f47041f3d17dc017f21ea" ftype="mothur.align"/>
120 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/> 124 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
121 <output name="name_out" md5="0c58174137c2ecabf7da9ab492ea46fc" ftype="mothur.names"/> 125 <output name="name_out" md5="0c58174137c2ecabf7da9ab492ea46fc" ftype="mothur.names"/>
122 </test> 126 </test>
123 <test><!-- test with oligos and all outputs --> 127 <test><!-- test with oligos and all outputs -->
124 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> 128 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
128 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 132 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
129 <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 133 <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
130 <param name="start" value="5"/> 134 <param name="start" value="5"/>
131 <param name="end" value="50"/> 135 <param name="end" value="50"/>
132 <expand macro="logfile-test"/> 136 <expand macro="logfile-test"/>
133 <ouptut name="pcr_fasta" md5="1e78af5a460572e22ce199e522a70388" ftype="mothur.align"/> 137 <output name="pcr_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
134 <output name="scrap_fasta" md5="0b63807f339dfd88cf958f7b069eba02" ftype="mothur.align"/> 138 <output name="scrap_fasta" md5="0b63807f339dfd88cf958f7b069eba02" ftype="mothur.align"/>
135 <output name="group_out" md5="301c358e61d38c83cc7382a8a210089a" ftype="mothur.groups"/> 139 <output name="group_out" md5="301c358e61d38c83cc7382a8a210089a" ftype="mothur.groups"/>
136 <output name="name_out" md5="62eb1162557408509c931496071add85" ftype="mothur.names"/> 140 <output name="name_out" md5="62eb1162557408509c931496071add85" ftype="mothur.names"/>
137 <output name="taxonomy_out" md5="4d72981cefd8b45d4f2793a28dccd9e4" ftype="mothur.seq.taxonomy"/> 141 <output name="taxonomy_out" md5="4d72981cefd8b45d4f2793a28dccd9e4" ftype="mothur.seq.taxonomy"/>
138 <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/> 142 <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/>
141 <help> 145 <help>
142 <![CDATA[ 146 <![CDATA[
143 147
144 @MOTHUR_OVERVIEW@ 148 @MOTHUR_OVERVIEW@
145 149
146 **Command Documenation** 150 **Command Documentation**
147 151
148 The pcr.seqs_ command assigns sequences to chosen taxonomy outline. 152 The pcr.seqs_ command assigns sequences to chosen taxonomy outline.
149 153
150 .. _pcr.seqs: http://www.mothur.org/wiki/Pcr.seqs 154 .. _pcr.seqs: https://www.mothur.org/wiki/Pcr.seqs
151 155
152 ]]> 156 ]]>
153 </help> 157 </help>
154 <expand macro="citations"/> 158 <expand macro="citations"/>
155 </tool> 159 </tool>