Mercurial > repos > iuc > mothur_make_sra

comparison make.sra.xml @ 3:215b28afd9dd 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 09:47:57 -0500
parents 2fed4f809b76
children 4aa5986d514f
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2:b28a5ca44ffa 3:215b28afd9dd
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 "$project" project.dat && 13 ln -s '$project' project.dat &&
14 ln -s "$sff" sff.dat && 14 ln -s '$sff' sff.dat &&
15 ln -s "$oligos" oligos.dat && 15 ln -s '$oligos' oligos.dat &&
16 ln -s "$mimark" mimark.dat && 16 ln -s '$mimark' mimark.dat &&
17 ln -s "$fastq" fastq.dat && 17 ln -s '$fastq' fastq.dat &&
18 18
19 echo 'make.sra( 19 echo 'make.sra(
20 project=project.dat, 20 project=project.dat,
21 sff=sff.dat, 21 sff=sff.dat,
22 oligos=oligos.dat, 22 oligos=oligos.dat,
23 mimark=mimark.dat, 23 mimark=mimark.dat,
24 #if $fastq: 24 #if $fastq:
25 fastq=fastq.dat, 25 fastq=fastq.dat,
26 #end if 26 #end if
27 bdiffs=$bdiffs, 27 bdiffs=$bdiffs,
28 pdiffs=$pdiffs, 28 pdiffs=$pdiffs,
29 tdiffs=$tdiffs, 29 tdiffs=$tdiffs,
30 ldiffs=$ldiffs, 30 ldiffs=$ldiffs,
31 sdiffs=$sdiffs, 31 sdiffs=$sdiffs,
32 checkorient=$checkorient, 32 checkorient=$checkorient,
33 orientation=$orientation, 33 orientation=$orientation,
34 platform=$platform, 34 platform=$platform,
35 instrument=$instrument, 35 instrument=$instrument,
36 libstrategy=$libstrategy, 36 libstrategy=$libstrategy,
37 libselection=$libselection, 37 libselection=$libselection,
38 libsource=$libsource, 38 libsource=$libsource,
39 datatype=$datatype 39 datatype=$datatype,
40 )' 40 trim=$trim,
41 | sed 's/ //g' ## mothur trips over whitespace 41 includescrap=$includescrap
42 | mothur 42 )'
43 | tee mothur.out.log 43 | sed 's/ //g' ## mothur trips over whitespace
44 | mothur
45 | tee mothur.out.log
44 ]]></command> 46 ]]></command>
45 <inputs> 47 <inputs>
46 <param name="project" type="data" format="tabular" label="Project file"/> 48 <param name="project" type="data" format="tabular" label="Project file"/>
47 <param name="sff" type="data" format="sff" label="sff - provide the original sff file"/> 49 <param name="sff" type="data" format="sff" label="sff - provide the original sff file"/>
48 <param name="oligos" type="data" format="mothur.oligos" label="oligos - provide an oligos file to parse your sff or fastq file by. It is required and must contain barcodes and primers"/> 50 <param name="oligos" type="data" format="mothur.oligos" label="oligos - provide an oligos file to parse your sff or fastq file by. It is required and must contain barcodes and primers"/>
156 <option value="EPIGENOMICS">EPIGENOMICS</option> 158 <option value="EPIGENOMICS">EPIGENOMICS</option>
157 <option value="PHENOTYPE">PHENOTYPE</option> 159 <option value="PHENOTYPE">PHENOTYPE</option>
158 <option value="GENOTYPE">GENOTYPE</option> 160 <option value="GENOTYPE">GENOTYPE</option>
159 <option value="OTHER">OTHER</option> 161 <option value="OTHER">OTHER</option>
160 </param> 162 </param>
163 <param name="trim" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Trim sequences and quality scores?" help="will trim to the clipQualLeft and clipQualRight values in sff file"/>
164 <param name="includescrap" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Include scrapped sequences in your submission?"/>
161 </inputs> 165 </inputs>
162 <outputs> 166 <outputs>
163 <expand macro="logfile-output"/> 167 <expand macro="logfile-output"/>
164 <data name="fasta_out" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta"/> 168 <data name="fasta_out" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta"/>
165 <data name="qual_out" format="qual" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual"/> 169 <data name="qual_out" format="qual" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual"/>
189 </assert_contents> 193 </assert_contents>
190 </output> 194 </output>
191 <expand macro="logfile-test"/> 195 <expand macro="logfile-test"/>
192 </test> 196 </test>
193 </tests> 197 </tests>
194 <help> 198 <help><![CDATA[
195 <![CDATA[
196 199
197 @MOTHUR_OVERVIEW@ 200 @MOTHUR_OVERVIEW@
198 201
199 **Command Documentation** 202 **Command Documentation**
200 203
201 The make.sra_ creates the necessary files for a NCBI submission. 204 The make.sra_ creates the necessary files for a NCBI submission.
202 205
203 .. _make.sra: https://www.mothur.org/wiki/Make.sra 206 .. _make.sra: https://www.mothur.org/wiki/Make.sra
204 207
205 ]]> 208 ]]></help>
206 </help>
207 <citations> 209 <citations>
208 <citation type="doi">10.1128/AEM.01541-09</citation> 210 <citation type="doi">10.1128/AEM.01541-09</citation>
209 </citations> 211 </citations>
210 </tool> 212 </tool>