Mercurial > repos > matthias > dada2_makesequencetable

comparison macros.xml @ 2:d2e7c5f8a9f7 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
author matthias
date Tue, 09 Apr 2019 07:10:43 -0400
parents 98e24c66eeb2
children c3834c230b0a
comparison
equal deleted inserted replaced
1:f2abdc9a849c 2:d2e7c5f8a9f7
13 <xml name="version_command"> 13 <xml name="version_command">
14 <version_command><![CDATA[ 14 <version_command><![CDATA[
15 echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 15 echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
16 ]]></version_command> 16 ]]></version_command>
17 </xml> 17 </xml>
18
19 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
20 18
21 <xml name="citations"> 19 <xml name="citations">
22 <citations> 20 <citations>
23 <citation type="doi">10.1038/nmeth.3869</citation> 21 <citation type="doi">10.1038/nmeth.3869</citation>
24 </citations> 22 </citations>
43 #end if 41 #end if
44 #end def 42 #end def
45 ]]></token> 43 ]]></token>
46 <!-- for filterAndTrim --> 44 <!-- for filterAndTrim -->
47 <xml name="trimmers"> 45 <xml name="trimmers">
48 <section name="trim" title="trimming parameters"> 46 <section name="trim" title="Trimming parameters">
49 <param name="truncQ" type="integer" value="2" min="0" label="Truncate reads at quality threshold" help="Truncate reads at the first instance of a quality score less than or equal to this threshold"/> 47 <param name="truncQ" type="integer" value="2" min="0" label="Truncate reads at quality threshold" help="Truncate reads at the first instance of a quality score less than or equal to this threshold"/>
50 <param name="truncLen" type="integer" value="0" min="0" label="Truncate read length" help=""/> 48 <param name="trimLeft" type="integer" value="0" min="0" label="Trim start of each read" help="The number of nucleotides to remove from the start of each read."/>
51 <param name="trimLeft" type="integer" value="0" min="0" label="Remove nucleotides from start" help=""/> 49 <param name="trimRight" type="integer" value="0" min="0" label="Trim end of each read" help="The number of nucleotides to remove from the end of each read"/>
52 <param name="trimRight" type="integer" value="0" min="0" label="Remove nucleotides from end" help=""/> 50 <param name="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded."/>
53 </section> 51 </section>
54 </xml> 52 </xml>
55 <xml name="filters"> 53 <xml name="filters">
56 <section name="filter" title="filtering parameters"> 54 <section name="filter" title="Filtering parameters">
57 <param name="maxLen" type="integer" value="" optional="true" min="0" label="Remove reads longer than" help=""/> 55 <param name="maxLen" type="integer" value="" optional="true" min="0" label="Remove long reads" help="Remove reads with length greater than this value. Default: no length threshold"/>
58 <param name="minLen" type="integer" value="20" min="0" label="Remove reads shorter than" help=""/> 56 <param name="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/>
59 <param name="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help=""/> 57 <param name="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help="Note that some of the subsequent dada pipeline steps do not allow Ns"/>
60 <param name="minQ" type="integer" value="0" min="0" label="Remove reads containing quality" help=""/> 58 <param name="minQ" type="integer" value="0" min="0" label="Remove low quality reads" help="Reads contain a quality score less than this value will be discarded"/>
61 <param name="maxEE" type="integer" value="" optional="true" min="0" label="Remove reads by expected errors" help=""/> 59 <param name="maxEE" type="integer" value="" optional="true" min="0" label="Remove reads by number expected errors" help="Reads with a higher number of expected errors (EE) will be discarded, where EE = sum(10^(-Q_i/10)), with Q are the nominal quality scores at the read positions"/>
62 </section> 60 </section>
63 </xml> 61 </xml>
64
65 62
66 <xml name="errorEstimationFunction"> 63 <xml name="errorEstimationFunction">
67 <param name="errfoo" type="select" label="Error function"> 64 <param name="errfoo" type="select" label="Error function">
68 <option value="loessErrfun">loess</option> 65 <option value="loessErrfun">loess</option>
69 <option value="noqualErrfun">noqual</option> 66 <option value="noqualErrfun">noqual</option>