Mercurial > repos > iuc > dada2_filterandtrim

comparison dada2_filterAndTrim.xml @ 2:23fc35093b11 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 07:33:38 -0400
parents cc41546adf56
children 34e55239e68b
comparison
equal deleted inserted replaced
1:777f9846c56d 2:23fc35093b11
80 minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.lowcomplex = $rmlowcomplex, 80 minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.lowcomplex = $rmlowcomplex,
81 rm.phix = $rmPhiX, orient.fwd = orientFwd) 81 rm.phix = $rmPhiX, orient.fwd = orientFwd)
82 82
83 rownames(ftout) <- c( '$paired_cond.reads.element_identifier' ) 83 rownames(ftout) <- c( '$paired_cond.reads.element_identifier' )
84 write.table(ftout, "$outtab", quote=F, sep="\t", col.names=NA) 84 write.table(ftout, "$outtab", quote=F, sep="\t", col.names=NA)
85
86 if(0 %in% ftout){
87 quit(save="no", status="1")
88 }
89
85 ]]></configfile> 90 ]]></configfile>
86 </configfiles> 91 </configfiles>
87 <inputs> 92 <inputs>
88 <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fwd" argument_rev="rev"/> 93 <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fwd" argument_rev="rev"/>
89 <expand macro="trimmers"/> 94 <expand macro="trimmers"/>
135 </conditional> 140 </conditional>
136 <output_collection name="paired_output" type="paired" count="2"> 141 <output_collection name="paired_output" type="paired" count="2">
137 <element name="forward" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> 142 <element name="forward" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
138 <element name="reverse" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" /> 143 <element name="reverse" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
139 </output_collection> 144 </output_collection>
140 <output name="outtab" value="filterAndTrim_F3D0.tab" ftype="tabular"/> 145 <!-- in the test the used collection (the pair) has the name "Unnamed collection" hence we have two lines difference. In the real world the pair will have the sample name, i.e its OK. To be sure we test for the counts as well -->
146 <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular" lines_diff="2">
147 <assert_contents>
148 <has_text text="745" />
149 <has_text text="750" />
150 </assert_contents>
151 </output>
141 </test> 152 </test>
142 <!-- paired data given separately --> 153 <!-- paired data given separately -->
143 <test expect_num_outputs="3"> 154 <test expect_num_outputs="3">
144 <conditional name="paired_cond"> 155 <conditional name="paired_cond">
145 <param name="paired_select" value="separate"/> 156 <param name="paired_select" value="separate"/>
146 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> 157 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
147 <param name="sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> 158 <param name="sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
148 </conditional> 159 </conditional>
149 <output name="output_fwd" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> 160 <output name="output_fwd" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
150 <output name="output_rev" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" /> 161 <output name="output_rev" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
151 <output name="outtab" value="filterAndTrim_F3D0.tab" ftype="tabular" compare="sim_size"/> 162 <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular"/>
152 </test> 163 </test>
153 <!-- single end data --> 164 <!-- single end data -->
154 <test expect_num_outputs="1"> 165 <test expect_num_outputs="1">
155 <conditional name="paired_cond"> 166 <conditional name="paired_cond">
156 <param name="paired_select" value="single"/> 167 <param name="paired_select" value="single"/>
211 <param name="seprev_cond|filter|minQ" value="13" /> 222 <param name="seprev_cond|filter|minQ" value="13" />
212 <param name="seprev_cond|filter|maxEE" value="1" /> 223 <param name="seprev_cond|filter|maxEE" value="1" />
213 <param name="output_statistics" value="FALSE" /> 224 <param name="output_statistics" value="FALSE" />
214 <output_collection name="paired_output" type="paired" count="2"/> 225 <output_collection name="paired_output" type="paired" count="2"/>
215 </test> 226 </test>
227
228 <!-- test failure in case all reads are filtered -->
229 <test expect_exit_code="1" expect_failure="true">
230 <conditional name="paired_cond" >
231 <param name="paired_select" value="paired"/>
232 <param name="reads">
233 <collection type="paired">
234 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
235 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
236 </collection>
237 </param>
238 </conditional>
239 <param name="filter|minLen" value="1000" />
240 <param name="output_statistics" value="FALSE" />
241 </test>
242
216 </tests> 243 </tests>
217 244
218 <help><![CDATA[ 245 <help><![CDATA[
219 Description 246 Description
220 ........... 247 ...........