Mercurial > repos > matthias > dada2_filterandtrim

comparison dada2_filterAndTrim.xml @ 5:ea57169fd0d0 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
author matthias
date Sun, 05 May 2019 12:28:14 -0400
parents e4b415aa4c84
children 37305bbf8f44
comparison
equal deleted inserted replaced
4:a01bd67c9e77 5:ea57169fd0d0
77 <param name="paired_select" type="select" label="Paired reads"> 77 <param name="paired_select" type="select" label="Paired reads">
78 <option value="TRUE">yes</option> 78 <option value="TRUE">yes</option>
79 <option value="FALSE">no</option> 79 <option value="FALSE">no</option>
80 </param> 80 </param>
81 <when value="TRUE"> 81 <when value="TRUE">
82 <param name="reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Paired short read data"/> 82 <param name="reads" argument="fwd/rev" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Paired short read data"/>
83 </when> 83 </when>
84 <when value="FALSE"> 84 <when value="FALSE">
85 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/> 85 <param name="reads" argument="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
86 </when> 86 </when>
87 </conditional> 87 </conditional>
88 <expand macro="trimmers"/> 88 <expand macro="trimmers"/>
89 <expand macro="filters"/> 89 <expand macro="filters"/>
90 <conditional name="seprev_cond"> 90 <conditional name="seprev_cond">
102 <param name="orientFwd" argument="orinent.fwd" type="text" value="" optional="true" label="String present at the start of valid reads" help="see below"/> 102 <param name="orientFwd" argument="orinent.fwd" type="text" value="" optional="true" label="String present at the start of valid reads" help="see below"/>
103 <param name="output_statistics" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Output statistics" help="Create extra table with the number of reads pre and post filtering" /> 103 <param name="output_statistics" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Output statistics" help="Create extra table with the number of reads pre and post filtering" />
104 </inputs> 104 </inputs>
105 <outputs> 105 <outputs>
106 <collection name="paired_output" type="paired"> 106 <collection name="paired_output" type="paired">
107 <data name="forward" format="fastqsanger.gz" from_work_dir="filt_forward.fastq.gz" /> 107 <data name="forward" format="fastqsanger.gz" />
108 <data name="reverse" format="fastqsanger.gz" from_work_dir="filt_reverse.fastq.gz" /> 108 <data name="reverse" format="fastqsanger.gz" />
109 <filter>paired_cond['paired_select'] == 'TRUE'</filter> 109 <filter>paired_cond['paired_select'] == "TRUE"</filter>
110 </collection> 110 </collection>
111 <data name="output" format="fastqsanger.gz" from_work_dir="filt_forward.fastq.gz"> 111 <data name="output" format="fastqsanger.gz" >
112 <filter>paired_cond['paired_select'] == 'FALSE'</filter> 112 <filter>paired_cond['paired_select'] == "FALSE"</filter>
113 </data> 113 </data>
114 <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics"> 114 <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics">
115 <filter>output_statistics</filter> 115 <filter>output_statistics</filter>
116 </data> 116 </data>
117 </outputs> 117 </outputs>
118 <tests> 118 <tests>
119 <!-- paired data --> 119 <!-- paired data
120 currently removed `expect_num_outputs="2"` because of https://github.com/galaxyproject/galaxy/pull/7894-->
120 <test> 121 <test>
121 <conditional name="paired_cond"> 122 <conditional name="paired_cond">
122 <param name="paired_select" value="TRUE"/> 123 <param name="paired_select" value="TRUE"/>
123 <param name="reads"> 124 <param name="reads">
124 <collection type="paired"> 125 <collection type="paired">
125 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> 126 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
126 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> 127 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
127 </collection> 128 </collection>
128 </param> 129 </param>
129 </conditional> 130 </conditional>
130 <output_collection name="paired_output" count="2"> 131 <output_collection name="paired_output" type="paired" count="2">
131 <element name="forward" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> 132 <element name="forward" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
132 <element name="reverse" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" /> 133 <element name="reverse" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
133 </output_collection> 134 </output_collection>
135 <output name="outtab" value="filterAndTrim_F3D0.tab" ftype="tabular"/>
134 </test> 136 </test>
135 <!-- single end data --> 137 <!-- single end data -->
136 <test> 138 <test expect_num_outputs="1">
137 <conditional name="paired_cond"> 139 <conditional name="paired_cond">
138 <param name="paired_select" value="FALSE"/> 140 <param name="paired_select" value="FALSE"/>
139 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> 141 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
140 </conditional> 142 </conditional>
143 <param name="output_statistics" value="FALSE" />
141 <output name="output" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> 144 <output name="output" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
142 </test> 145 </test>
143 <!-- single end data trimming --> 146 <!-- single end data trimming -->
144 <test> 147 <test expect_num_outputs="1">
145 <conditional name="paired_cond"> 148 <conditional name="paired_cond">
146 <param name="paired_select" value="FALSE"/> 149 <param name="paired_select" value="FALSE"/>
147 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> 150 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
148 </conditional> 151 </conditional>
149 <param name="trim|truncQ" value="30" /> 152 <param name="trim|truncQ" value="30" />
150 <param name="trim|trimLeft" value="150" /> 153 <param name="trim|trimLeft" value="150" />
151 <param name="trim|trimRight" value="2" /> 154 <param name="trim|trimRight" value="2" />
152 <param name="trim|truncLen" value="2" /> 155 <param name="trim|truncLen" value="2" />
156 <param name="output_statistics" value="FALSE" />
153 <output name="output" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> 157 <output name="output" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
154 </test> 158 </test>
155 <!-- single end data filtering --> 159 <!-- single end data filtering -->
156 <test> 160 <test expect_num_outputs="1">
157 <conditional name="paired_cond"> 161 <conditional name="paired_cond">
158 <param name="paired_select" value="FALSE"/> 162 <param name="paired_select" value="FALSE"/>
159 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> 163 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
160 </conditional> 164 </conditional>
161 <param name="filter|maxLen" value="255" /> 165 <param name="filter|maxLen" value="255" />
162 <param name="filter|minLen" value="60" /> 166 <param name="filter|minLen" value="60" />
163 <param name="filter|maxN" value="100" /> 167 <param name="filter|maxN" value="100" />
164 <param name="filter|minQ" value="13" /> 168 <param name="filter|minQ" value="13" />
165 <param name="filter|maxEE" value="1" /> 169 <param name="filter|maxEE" value="1" />
170 <param name="output_statistics" value="FALSE" />
166 <output name="output" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> 171 <output name="output" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
167 </test> 172 </test>
168 <!-- paired data w separate filters and trimmers for reverse --> 173 <!-- paired data w separate filters and trimmers for reverse
169 <test> 174 currently removed `expect_num_outputs="1"` because of https://github.com/galaxyproject/galaxy/pull/7894-->
175 <test>
170 <conditional name="paired_cond"> 176 <conditional name="paired_cond">
171 <param name="paired_select" value="TRUE"/> 177 <param name="paired_select" value="TRUE"/>
172 <param name="reads"> 178 <param name="reads">
173 <collection type="paired"> 179 <collection type="paired">
174 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> 180 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
184 <param name="seprev_cond|filter|maxLen" value="255" /> 190 <param name="seprev_cond|filter|maxLen" value="255" />
185 <param name="seprev_cond|filter|minLen" value="60" /> 191 <param name="seprev_cond|filter|minLen" value="60" />
186 <param name="seprev_cond|filter|maxN" value="100" /> 192 <param name="seprev_cond|filter|maxN" value="100" />
187 <param name="seprev_cond|filter|minQ" value="13" /> 193 <param name="seprev_cond|filter|minQ" value="13" />
188 <param name="seprev_cond|filter|maxEE" value="1" /> 194 <param name="seprev_cond|filter|maxEE" value="1" />
189 <output_collection name="paired_output" count="2"/> 195 <param name="output_statistics" value="FALSE" />
196 <output_collection name="paired_output" type="paired" count="2"/>
190 </test> 197 </test>
191 </tests> 198 </tests>
192 199
193 <help><![CDATA[ 200 <help><![CDATA[
194 Description 201 Description