Mercurial > repos > iuc > dada2_mergepairs

comparison dada2_mergePairs.xml @ 9:35176674168c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 9bbc0898b9bbe73c7fc60ac162d80d749a7f97c1
author iuc
date Fri, 24 May 2024 11:45:13 +0000
parents 84743da21318
children
comparison
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8:06be32772107 9:35176674168c
18 dadaR <- readRDS('$dadaR') 18 dadaR <- readRDS('$dadaR')
19 19
20 merged <- mergePairs(dadaF, '$derepF', dadaR, '$derepR', minOverlap = $minOverlap, maxMismatch = $maxMismatch, 20 merged <- mergePairs(dadaF, '$derepF', dadaR, '$derepR', minOverlap = $minOverlap, maxMismatch = $maxMismatch,
21 ## currently not accessible by the wrapper returnRejects = FALSE, propagateCol = character(0), 21 ## currently not accessible by the wrapper returnRejects = FALSE, propagateCol = character(0),
22 justConcatenate = $justConcatenate, trimOverhang = $trimOverhang) 22 justConcatenate = $justConcatenate, trimOverhang = $trimOverhang)
23
24 saveRDS(merged, file='$merged') 23 saveRDS(merged, file='$merged')
25 ##For display in Galaxy this could be transposed (..but the user could also do it herself) 24 #if $output_details
26 ##write.table(merged, "$merged", quote=F, sep="\t", row.names = F, col.names = T) 25 ##For display in Galaxy this could be transposed (..but the user could also do it herself)
26 merged <- apply(merged, 2, as.character)
27 write.table(merged, "$merged_details", quote=F, sep="\t", row.names = F, col.names = T)
28 #end if
27 ]]></configfile> 29 ]]></configfile>
28 </configfiles> 30 </configfiles>
29 <inputs> 31 <inputs>
30 <param argument="dadaF" type="data" format="dada2_dada" label="Dada results for forward reads"/> 32 <param argument="dadaF" type="data" format="dada2_dada" label="Dada results for forward reads"/>
31 <param argument="derepF" type="data" format="fastq,fastq.gz" label="Forward reads" help="despite the parameter name the sequences don't need to be dereplicated "/> 33 <param argument="derepF" type="data" format="fastq,fastq.gz" label="Forward reads" help="despite the parameter name the sequences don't need to be dereplicated "/>
33 <param argument="derepR" type="data" format="fastq,fastq.gz" label="Reverse reads" help="despite the parameter name the sequences don't need to be dereplicated "/> 35 <param argument="derepR" type="data" format="fastq,fastq.gz" label="Reverse reads" help="despite the parameter name the sequences don't need to be dereplicated "/>
34 <param argument="minOverlap" type="integer" value="12" min="0" label="Minimum length of the overlap"/> 36 <param argument="minOverlap" type="integer" value="12" min="0" label="Minimum length of the overlap"/>
35 <param argument="maxMismatch" type="integer" value="0" min="0" label="Maximum number of mismatches"/> 37 <param argument="maxMismatch" type="integer" value="0" min="0" label="Maximum number of mismatches"/>
36 <param argument="justConcatenate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Concatenated rather than merge" help="The forward and reverse-complemented reverse read are concatenated rather than merged, with a 10 Ns spacer inserted between them"/> 38 <param argument="justConcatenate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Concatenated rather than merge" help="The forward and reverse-complemented reverse read are concatenated rather than merged, with a 10 Ns spacer inserted between them"/>
37 <param argument="trimOverhang" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Trim overhangs" help="Overhangs are when the reverse read extends past the start of the forward read, and vice-versa, as can happen when reads are longer than the amplicon and read into the other-direction primer region"/> 39 <param argument="trimOverhang" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Trim overhangs" help="Overhangs are when the reverse read extends past the start of the forward read, and vice-versa, as can happen when reads are longer than the amplicon and read into the other-direction primer region"/>
40 <param name="output_details" type="boolean" label="Output detailed table" help="Contains detailed information on the merged sequences, e.g. number of matched/mismatches"/>
38 </inputs> 41 </inputs>
39 <outputs> 42 <outputs>
40 <data name="merged" format="dada2_mergepairs" label="${tool.name} on ${on_string}"/> 43 <data name="merged" format="dada2_mergepairs" label="${tool.name} on ${on_string}"/>
44 <data name="merged_details" format="tabular" label="${tool.name} on ${on_string}: details">
45 <filter>output_details</filter>
46 </data>
41 </outputs> 47 </outputs>
42 <tests> 48 <tests>
43 <test> 49 <test expect_num_outputs="1">
44 <param name="dadaF" ftype="dada2_dada" value="dada_F3D0_S188_L001_R1.Rdata"/> 50 <param name="dadaF" ftype="dada2_dada" value="dada_F3D0_S188_L001_R1.Rdata"/>
45 <param name="derepF" ftype="fastq.gz" value="filterAndTrim_F3D0_R1.fq.gz"/> 51 <param name="derepF" ftype="fastq.gz" value="filterAndTrim_F3D0_R1.fq.gz"/>
46 <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_S188_L001_R2.Rdata"/> 52 <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_S188_L001_R2.Rdata"/>
47 <param name="derepR" ftype="fastq.gz" value="filterAndTrim_F3D0_R2.fq.gz"/> 53 <param name="derepR" ftype="fastq.gz" value="filterAndTrim_F3D0_R2.fq.gz"/>
48 <output name="merged" value="mergePairs_F3D0_S188_L001.Rdata" ftype="dada2_mergepairs" compare="sim_size" delta="400" /> 54 <output name="merged" value="mergePairs_F3D0_S188_L001.Rdata" ftype="dada2_mergepairs" compare="sim_size" delta="400" />
49 </test> 55 </test>
50 <!-- test non-default options --> 56 <!-- test non-default options -->
51 <test> 57 <test expect_num_outputs="2">
52 <param name="dadaF" ftype="dada2_dada" value="dada_F3D0_S188_L001_R1.Rdata"/> 58 <param name="dadaF" ftype="dada2_dada" value="dada_F3D0_S188_L001_R1.Rdata"/>
53 <param name="derepF" ftype="fastq.gz" value="filterAndTrim_F3D0_R1.fq.gz"/> 59 <param name="derepF" ftype="fastq.gz" value="filterAndTrim_F3D0_R1.fq.gz"/>
54 <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_S188_L001_R2.Rdata"/> 60 <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_S188_L001_R2.Rdata"/>
55 <param name="derepR" ftype="fastq.gz" value="filterAndTrim_F3D0_R2.fq.gz"/> 61 <param name="derepR" ftype="fastq.gz" value="filterAndTrim_F3D0_R2.fq.gz"/>
56 <output name="merged" value="mergePairs_F3D0_S188_L001_nondefault.Rdata" ftype="dada2_mergepairs" compare="sim_size" delta="700"/> 62 <output name="merged" value="mergePairs_F3D0_S188_L001_nondefault.Rdata" ftype="dada2_mergepairs" compare="sim_size" delta="700"/>
57 <param name="minOverlap" value="8" /> 63 <param name="minOverlap" value="8" />
58 <param name="maxMismatch" value="1"/> 64 <param name="maxMismatch" value="1"/>
59 <param name="justConcatenate" value="TRUE" /> 65 <param name="justConcatenate" value="TRUE" />
60 <param name="trimOverhang" value="TRUE" /> 66 <param name="trimOverhang" value="TRUE" />
67 <param name="output_details" value="true"/>
68 <output name="merged_details">
69 <assert_contents>
70 <has_n_lines n="50"/>
71 <has_n_columns n="9"/>
72 </assert_contents>
73 </output>
61 </test> 74 </test>
62 </tests> 75 </tests>
63 <help><![CDATA[ 76 <help><![CDATA[
64 Description 77 Description
65 ........... 78 ...........