Mercurial > repos > iuc > dada2_filterandtrim

comparison dada2_filterAndTrim.xml @ 10:3efaa80a3e20 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 commit f65944aa0547c2fbe4b746cf443c85b2a76e9a48
author iuc
date Sat, 20 Dec 2025 14:09:18 +0000
parents 46ca7fe29b3e
children
comparison
equal deleted inserted replaced
9:46ca7fe29b3e 10:3efaa80a3e20
61 #if $paired_cond.paired_select == "paired" 61 #if $paired_cond.paired_select == "paired"
62 fwd <- c(fwd, '$paired_cond.reads.forward') 62 fwd <- c(fwd, '$paired_cond.reads.forward')
63 rev <- c(rev, '$paired_cond.reads.reverse') 63 rev <- c(rev, '$paired_cond.reads.reverse')
64 filt.fwd <- c(filt.fwd, '$paired_output.forward') 64 filt.fwd <- c(filt.fwd, '$paired_output.forward')
65 filt.rev <- c(filt.rev, '$paired_output.reverse') 65 filt.rev <- c(filt.rev, '$paired_output.reverse')
66 #else if $paired_cond.paired_select == "separate"
67 fwd <- c(fwd, '$paired_cond.reads')
68 rev <- c(rev, '$paired_cond.sdaer')
69 filt.fwd <- c(filt.fwd, '$output_fwd')
70 filt.rev <- c(filt.rev, '$output_rev')
71 #else 66 #else
72 fwd <- c(fwd, '$paired_cond.reads') 67 fwd <- c(fwd, '$paired_cond.reads')
73 filt.fwd <- c(filt.fwd, '$output_single') 68 filt.fwd <- c(filt.fwd, '$output_single')
74 #end if 69 #end if
75 70
120 <filter>paired_cond['paired_select'] == "paired"</filter> 115 <filter>paired_cond['paired_select'] == "paired"</filter>
121 </collection> 116 </collection>
122 <data name="output_single" format_source="paired_cond|reads" label="${tool.name} on ${on_string}: Reads" > 117 <data name="output_single" format_source="paired_cond|reads" label="${tool.name} on ${on_string}: Reads" >
123 <filter>paired_cond['paired_select'] == "single"</filter> 118 <filter>paired_cond['paired_select'] == "single"</filter>
124 </data> 119 </data>
125 <data name="output_fwd" format_source="paired_cond|reads" default_identifier_source="paired_cond|reads" label="${tool.name} on ${on_string}: Forward reads" >
126 <filter>paired_cond['paired_select'] == "separate"</filter>
127 </data>
128 <data name="output_rev" format_source="paired_cond|sdaer" default_identifier_source="paired_cond|sdaer" label="${tool.name} on ${on_string}: Reverse reads" >
129 <filter>paired_cond['paired_select'] == "separate"</filter>
130 </data>
131 <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics"> 120 <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics">
132 <filter>output_statistics</filter> 121 <filter>output_statistics</filter>
133 </data> 122 </data>
134 </outputs> 123 </outputs>
135 <tests> 124 <tests>
154 <has_text text="745" /> 143 <has_text text="745" />
155 <has_text text="750" /> 144 <has_text text="750" />
156 </assert_contents> 145 </assert_contents>
157 </output> 146 </output>
158 </test> 147 </test>
159 <!-- paired data given separately -->
160 <test expect_num_outputs="3">
161 <conditional name="paired_cond">
162 <param name="paired_select" value="separate"/>
163 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
164 <param name="sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
165 </conditional>
166 <output name="output_fwd" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
167 <output name="output_rev" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
168 <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular"/>
169 </test>
170 <!-- single end data --> 148 <!-- single end data -->
171 <test expect_num_outputs="1"> 149 <test expect_num_outputs="1">
172 <conditional name="paired_cond"> 150 <conditional name="paired_cond">
173 <param name="paired_select" value="single"/> 151 <param name="paired_select" value="single"/>
174 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> 152 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
175 </conditional> 153 </conditional>
176 <param name="rmPhiX" value="TRUE" /> 154 <param name="rmPhiX" value="TRUE" />
177 <param name="rmlowcomplex" value="2" /> 155 <param name="rmlowcomplex" value="2" />
178 <param name="orientFwd" value="TACGG" /> 156 <param name="orientFwd" value="TACGG" />
179 <param name="output_statistics" value="FALSE" /> 157 <param name="output_statistics" value="FALSE" />
180 <output name="output_fwd" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> 158 <output name="output_single" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
181 </test> 159 </test>
182 <!-- single end data trimming --> 160 <!-- single end data trimming -->
183 <test expect_num_outputs="1"> 161 <test expect_num_outputs="1">
184 <conditional name="paired_cond"> 162 <conditional name="paired_cond">
185 <param name="paired_select" value="single"/> 163 <param name="paired_select" value="single"/>
188 <param name="trim|truncQ" value="30" /> 166 <param name="trim|truncQ" value="30" />
189 <param name="trim|trimLeft" value="150" /> 167 <param name="trim|trimLeft" value="150" />
190 <param name="trim|trimRight" value="2" /> 168 <param name="trim|trimRight" value="2" />
191 <param name="trim|truncLen" value="2" /> 169 <param name="trim|truncLen" value="2" />
192 <param name="output_statistics" value="FALSE" /> 170 <param name="output_statistics" value="FALSE" />
193 <output name="output_fwd" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> 171 <output name="output_single" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
194 </test> 172 </test>
195 <!-- single end data filtering --> 173 <!-- single end data filtering -->
196 <test expect_num_outputs="1"> 174 <test expect_num_outputs="1">
197 <conditional name="paired_cond"> 175 <conditional name="paired_cond">
198 <param name="paired_select" value="single"/> 176 <param name="paired_select" value="single"/>
202 <param name="filter|minLen" value="60" /> 180 <param name="filter|minLen" value="60" />
203 <param name="filter|maxN" value="100" /> 181 <param name="filter|maxN" value="100" />
204 <param name="filter|minQ" value="13" /> 182 <param name="filter|minQ" value="13" />
205 <param name="filter|maxEE" value="1" /> 183 <param name="filter|maxEE" value="1" />
206 <param name="output_statistics" value="FALSE" /> 184 <param name="output_statistics" value="FALSE" />
207 <output name="output_fwd" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> 185 <output name="output_single" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
208 </test> 186 </test>
209 <!-- paired data w separate filters and trimmers for reverse --> 187 <!-- paired data w separate filters and trimmers for reverse -->
210 <test expect_num_outputs="3"> 188 <test expect_num_outputs="3">
211 <conditional name="paired_cond" > 189 <conditional name="paired_cond" >
212 <param name="paired_select" value="paired"/> 190 <param name="paired_select" value="paired"/>