Mercurial > repos > iuc > dada2_assigntaxonomyaddspecies

comparison dada2_assignTaxonomyAddspecies.xml @ 2:1c9715cef808 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
author iuc
date Mon, 16 Mar 2020 08:03:24 -0400
parents 18517edb4733
children 76d3d2b10738
comparison
equal deleted inserted replaced
1:4d89978c6188 2:1c9715cef808
27 ref <- '$reference_cond.refFasta.fields.path' 27 ref <- '$reference_cond.refFasta.fields.path'
28 tl <- '$reference_cond.refFasta.fields.taxlevels' 28 tl <- '$reference_cond.refFasta.fields.taxlevels'
29 #end if 29 #end if
30 tl <- strsplit(tl, ",")[[1]] 30 tl <- strsplit(tl, ",")[[1]]
31 31
32 #if str($seed)
33 set.seed($seed)
34 #end if
35
32 taxa <- assignTaxonomy(seqs, ref, minBoot = $minBoot, tryRC = $tryRC, 36 taxa <- assignTaxonomy(seqs, ref, minBoot = $minBoot, tryRC = $tryRC,
33 outputBootstraps = $outputBootstraps, 37 outputBootstraps = $outputBootstraps,
34 taxLevels = tl, multithread = nthreads, verbose=T) 38 taxLevels = tl, multithread = nthreads, verbose=T)
35 39
36 #if $outputBootstraps 40 #if $outputBootstraps
51 #end if 55 #end if
52 taxa <- addSpecies(taxa, ref, allowMultiple = aM, tryRC = $addSpecies_cond.tryRC) 56 taxa <- addSpecies(taxa, ref, allowMultiple = aM, tryRC = $addSpecies_cond.tryRC)
53 #end if 57 #end if
54 write.table(taxa, file = '$output', quote = F, sep = "\t", row.names = T, col.names = NA) 58 write.table(taxa, file = '$output', quote = F, sep = "\t", row.names = T, col.names = NA)
55 59
56 #if $outputBootstraps 60 #if $outputBootstraps == "TRUE"
57 write.table(boot, file = '$bootstraps', quote = F, sep = "\t", row.names = T, col.names = NA) 61 write.table(boot, file = '$bootstraps', quote = F, sep = "\t", row.names = T, col.names = NA)
58 #end if 62 #end if
59 ]]></configfile> 63 ]]></configfile>
60 </configfiles> 64 </configfiles>
61 <inputs> 65 <inputs>
120 </when> 124 </when>
121 </conditional> 125 </conditional>
122 <param argument="tryRC" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Try reverse complement" help="the reverse-complement of each sequence will be used for classification if it is a better match to the reference sequences than the forward sequence"/> 126 <param argument="tryRC" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Try reverse complement" help="the reverse-complement of each sequence will be used for classification if it is a better match to the reference sequences than the forward sequence"/>
123 </when> 127 </when>
124 </conditional> 128 </conditional>
129 <param name="seed" type="integer" value="" optional="true" label="Seed" help="Seed for the random number renerator. Set it in order to reproduce exactly the same results."/>
125 </inputs> 130 </inputs>
126 <outputs> 131 <outputs>
127 <data name="output" format="tabular" label="${tool.name} on ${on_string}"/> 132 <data name="output" format="tabular" label="${tool.name} on ${on_string}"/>
128 <data name="bootstraps" format="tabular" label="${tool.name} on ${on_string}: bootstraps"> 133 <data name="bootstraps" format="tabular" label="${tool.name} on ${on_string}: bootstraps">
129 <filter>outputBootstraps</filter> 134 <filter>outputBootstraps</filter>
130 </data> 135 </data>
131 </outputs> 136 </outputs>
132 <tests> 137 <tests>
133 <!-- test w default params --> 138 <!-- test w default params -->
134 <test expect_num_outputs="1"> 139 <test expect_num_outputs="1">
135 <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/> 140 <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo.tab"/>
136 <param name="reference_cond|reference_select" value="history"/> 141 <param name="reference_cond|reference_select" value="history"/>
137 <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa"/> 142 <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa.gz"/>
138 <param name="reference_cond|taxLevels" value="Level1,Level2,Level3,Level4,Level5" /> 143 <param name="reference_cond|taxLevels" value="Level1,Level2,Level3,Level4,Level5" />
139 <param name="addSpecies_cond|addSpecies_select" value="TRUE"/> 144 <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
140 <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/> 145 <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/>
141 <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa" /> 146 <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa.gz" />
142 <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" /> 147 <param name="seed" value="42"/>
148 <output name="output" value="assignTaxonomyAddspecies.tab" ftype="tabular" compare="sim_size" delta="0"/>
143 </test> 149 </test>
144 <!-- test w default params, bulit in reference --> 150 <!-- test w default params, bulit in reference -->
145 <test expect_num_outputs="1"> 151 <test expect_num_outputs="2">
146 <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/> 152 <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo.tab"/>
147 <param name="reference_cond|reference_select" value="builtin"/> 153 <param name="reference_cond|reference_select" value="builtin"/>
148 <param name="reference_cond|refFasta" value="test_buildid"/> 154 <param name="reference_cond|refFasta" value="test_buildid"/>
155 <param name="outputBootstraps" value="TRUE" />
149 <param name="addSpecies_cond|addSpecies_select" value="TRUE"/> 156 <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
150 <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="builtin"/> 157 <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="builtin"/>
151 <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" value="test_buildid" /> 158 <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" value="test_buildid" />
152 <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" /> 159 <param name="seed" value="42"/>
160 <output name="output" value="assignTaxonomyAddspecies.tab" ftype="tabular" compare="sim_size" delta="0" />
161 <output name="bootstraps" value="assignTaxonomyAddspecies_boot.tab" ftype="tabular" compare="sim_size" delta="100" />
153 </test> 162 </test>
154 <!-- test w output bootstraps, minRC, note: sim_size for bootstraps output due to the probabilistics --> 163 <!-- minRC, note: sim_size for bootstraps output due to the probabilistics -->
155 <test expect_num_outputs="2"> 164 <test expect_num_outputs="1">
156 <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/> 165 <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo.tab"/>
157 <param name="reference_cond|reference_select" value="history"/> 166 <param name="reference_cond|reference_select" value="history"/>
158 <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa"/> 167 <param name="reference_cond|refFasta" ftype="fasta.gz" value="reference.fa.gz"/>
159 <param name="reference_cond|taxLevels" value="Level1,Level2,Level3,Level4,Level5" /> 168 <param name="reference_cond|taxLevels" value="Level1,Level2,Level3,Level4,Level5" />
160 <param name="minBoot" value="42" /> 169 <param name="minBoot" value="42" />
161 <param name="tryRC" value="TRUE" /> 170 <param name="tryRC" value="TRUE" />
162 <param name="outputBootstraps" value="TRUE" />
163 <param name="addSpecies_cond|addSpecies_select" value="TRUE"/> 171 <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
164 <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/> 172 <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/>
165 <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa" /> 173 <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta.gz" value="reference_species.fa.gz" />
166 <param name="addSpecies_cond|allowMultiple" value="TRUE"/> 174 <param name="addSpecies_cond|allowMultiple" value="TRUE"/>
167 <param name="addSpecies_cond|tryRC" value="TRUE" /> 175 <param name="addSpecies_cond|tryRC" value="TRUE" />
168 <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" compare="sim_size" /> 176 <param name="seed" value="42"/>
169 <output name="bootstraps" value="assignTaxonomyAddspecies_F3D0_boot.tab" ftype="tabular" compare="sim_size" /> 177 <output name="output" value="assignTaxonomyAddspecies.tab" ftype="tabular" compare="sim_size" />
170 </test> 178 </test>
171 </tests> 179 </tests>
172 <help><![CDATA[ 180 <help><![CDATA[
173 Description 181 Description
174 ........... 182 ...........