Mercurial > repos > jdv > porechop

comparison porechop.xml @ 2:f84a33bc5c3e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 19e515145381f7a8b16662e33678df7087019f19
author jdv
date Sat, 14 Oct 2017 10:52:30 -0400
parents 3cf98e7f21b7
children 80408ff0c1f5
comparison
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1:3cf98e7f21b7 2:f84a33bc5c3e
25 25
26 porechop 26 porechop
27 27
28 --input ${input} 28 --input ${input}
29 29
30 --format ${out_format}
31
30 #if str($demux_section.demux_options.demux) == "yes": 32 #if str($demux_section.demux_options.demux) == "yes":
31 --barcode_dir out 33 --barcode_dir out
32 #else: 34 #else:
33 --output "out/$filename" 35 --output "out/$filename"
34 #end if 36 #end if
82 <!-- ***************************************************************** --> 84 <!-- ***************************************************************** -->
83 85
84 <inputs> 86 <inputs>
85 87
86 <param argument="--input" type="data" format="fastq,fasta" label="Input reads" /> 88 <param argument="--input" type="data" format="fastq,fasta" label="Input reads" />
89
90 <param name="out_format" type="select" label="Output format">
91 <option value="fastq" selected="true">fastq</option>
92 <option value="fasta">fasta</option>
93 </param>
87 94
88 <section name="demux_section" title="Demultiplexing Options" expanded="True"> 95 <section name="demux_section" title="Demultiplexing Options" expanded="True">
89 <conditional name="demux_options"> 96 <conditional name="demux_options">
90 <param name="demux" type="select" label="Perform demultiplexing" help=""> 97 <param name="demux" type="select" label="Perform demultiplexing" help="">
91 <option value="no" selected="true">no</option> 98 <option value="no" selected="true">no</option>
134 141
135 <collection type="list" name="output"> 142 <collection type="list" name="output">
136 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="out" format="fastqsanger" /> 143 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="out" format="fastqsanger" />
137 </collection> 144 </collection>
138 145
146
147 <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string}">
148 <filter>out_format == 'fastq'</filter>
149 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="out" format="fastqsanger" />
150 </collection>
151 <collection type="list" name="output_collection_fasta" label="${tool.name} on ${on_string}">
152 <filter>out_format == 'fasta'</filter>
153 <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="out" format="fasta" />
154 </collection>
155
139 </outputs> 156 </outputs>
140 157
141 <!-- ***************************************************************** --> 158 <!-- ***************************************************************** -->
142 159
143 <tests> 160 <tests>
144 <test> 161 <test>
145 <param name="input" value="test_barcodes.fastq" ftype="fastq" /> 162 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
146 <param name="demux" value="yes" /> 163 <param name="demux" value="yes" />
147 <output_collection name="output" type="list"> 164 <output_collection name="output_collection_fastq" type="list">
148 <element name="BC01.fastq" file="bar1/BC01.fastq" compare="diff" decompress="true"/> 165 <element name="BC01.fastq" file="bar1/BC01.fastq" compare="diff" decompress="true"/>
149 <element name="BC02.fastq" file="bar1/BC02.fastq" compare="diff" decompress="true"/> 166 <element name="BC02.fastq" file="bar1/BC02.fastq" compare="diff" decompress="true"/>
150 <element name="BC03.fastq" file="bar1/BC03.fastq" compare="diff" decompress="true"/> 167 <element name="BC03.fastq" file="bar1/BC03.fastq" compare="diff" decompress="true"/>
151 <element name="none.fastq" file="bar1/none.fastq" compare="diff" decompress="true"/> 168 <element name="none.fastq" file="bar1/none.fastq" compare="diff" decompress="true"/>
152 </output_collection> 169 </output_collection>
153 </test> 170 </test>
154 <test> 171 <test>
155 <param name="input" value="test_barcodes.fastq" ftype="fastq" /> 172 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
156 <param name="demux" value="yes" /> 173 <param name="demux" value="yes" />
157 <param name="require_two_barcodes" value="True" /> 174 <param name="require_two_barcodes" value="True" />
158 <output_collection name="output" type="list"> 175 <output_collection name="output_collection_fastq" type="list">
159 <element name="BC01.fastq" file="bar2/BC01.fastq" compare="diff" decompress="true"/> 176 <element name="BC01.fastq" file="bar2/BC01.fastq" compare="diff" decompress="true"/>
160 <element name="BC02.fastq" file="bar2/BC02.fastq" compare="diff" decompress="true"/> 177 <element name="BC02.fastq" file="bar2/BC02.fastq" compare="diff" decompress="true"/>
161 <element name="BC03.fastq" file="bar2/BC03.fastq" compare="diff" decompress="true"/> 178 <element name="BC03.fastq" file="bar2/BC03.fastq" compare="diff" decompress="true"/>
162 <element name="none.fastq" file="bar2/none.fastq" compare="diff" decompress="true"/> 179 <element name="none.fastq" file="bar2/none.fastq" compare="diff" decompress="true"/>
163 </output_collection> 180 </output_collection>
164 </test> 181 </test>
165 <test> 182 <test>
166 <param name="input" value="test_barcodes.fastq" ftype="fastq" /> 183 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
167 <param name="demux" value="yes" /> 184 <param name="demux" value="yes" />
168 <param name="trim" value="yes" /> 185 <param name="trim" value="yes" />
169 <output_collection name="output" type="list"> 186 <output_collection name="output_collection_fastq" type="list">
170 <element name="BC01.fastq" file="bar1_trim/BC01.fastq" compare="diff" decompress="true"/> 187 <element name="BC01.fastq" file="bar1_trim/BC01.fastq" compare="diff" decompress="true"/>
171 <element name="BC02.fastq" file="bar1_trim/BC02.fastq" compare="diff" decompress="true"/> 188 <element name="BC02.fastq" file="bar1_trim/BC02.fastq" compare="diff" decompress="true"/>
172 <element name="BC03.fastq" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/> 189 <element name="BC03.fastq" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/>
173 <element name="none.fastq" file="bar1_trim/none.fastq" compare="diff" decompress="true"/> 190 <element name="none.fastq" file="bar1_trim/none.fastq" compare="diff" decompress="true"/>
174 </output_collection> 191 </output_collection>