Mercurial > repos > iuc > mothur_make_sra

comparison make.sra.xml @ 1:2fed4f809b76 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 04:24:24 -0400
parents 2d09b22f4a95
children 215b28afd9dd
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0:2d09b22f4a95 1:2fed4f809b76
2 <description>creates the necessary files for a NCBI submission</description> 2 <description>creates the necessary files for a NCBI submission</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 "$project" project.dat && 13 ln -s "$project" project.dat &&
11 ln -s "$sff" sff.dat && 14 ln -s "$sff" sff.dat &&
12 ln -s "$oligos" oligos.dat && 15 ln -s "$oligos" oligos.dat &&
13 ln -s "$mimark" mimark.dat && 16 ln -s "$mimark" mimark.dat &&
35 libsource=$libsource, 38 libsource=$libsource,
36 datatype=$datatype 39 datatype=$datatype
37 )' 40 )'
38 | sed 's/ //g' ## mothur trips over whitespace 41 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur 42 | mothur
43 | tee mothur.out.log
40 ]]></command> 44 ]]></command>
41 <inputs> 45 <inputs>
42 <param name="project" type="data" format="tabular" label="Project file"/> 46 <param name="project" type="data" format="tabular" label="Project file"/>
43 <param name="sff" type="data" format="sff" label="sff - provide the original sff file"/> 47 <param name="sff" type="data" format="sff" label="sff - provide the original sff file"/>
44 <param name="oligos" type="data" format="mothur.oligos" label="oligos - provide an oligos file to parse your sff or fastq file by. It is required and must contain barcodes and primers"/> 48 <param name="oligos" type="data" format="mothur.oligos" label="oligos - provide an oligos file to parse your sff or fastq file by. It is required and must contain barcodes and primers"/>
190 <help> 194 <help>
191 <![CDATA[ 195 <![CDATA[
192 196
193 @MOTHUR_OVERVIEW@ 197 @MOTHUR_OVERVIEW@
194 198
195 **Command Documenation** 199 **Command Documentation**
196 200
197 The make.sra_ creates the necessary files for a NCBI submission. 201 The make.sra_ creates the necessary files for a NCBI submission.
198 202
199 .. _make.sra: http://www.mothur.org/wiki/Make.sra 203 .. _make.sra: https://www.mothur.org/wiki/Make.sra
200 204
201 ]]> 205 ]]>
202 </help> 206 </help>
203 <citations> 207 <citations>
204 <citation type="doi">10.1128/AEM.01541-09</citation> 208 <citation type="doi">10.1128/AEM.01541-09</citation>