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comparison porechop.xml @ 9:e3ad639c692a draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit 83364d7d78ca5524a08065daef995bfcd54a379d-dirty
author jdv
date Fri, 01 Dec 2017 21:27:15 -0500
parents 852b3fe95c20
children 0cb1ba651e9e
comparison
equal deleted inserted replaced
8:852b3fe95c20 9:e3ad639c692a
131 131
132 <outputs> 132 <outputs>
133 133
134 <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string}"> 134 <collection type="list" name="output_collection_fastq" label="${tool.name} on ${on_string}">
135 <filter>out_format == 'fastq'</filter> 135 <filter>out_format == 'fastq'</filter>
136 <filter>demux_section['demux_options']['demux'] == 'yes'</filter>
136 <discover_datasets pattern="__designation_and_ext__" directory="out" format="fastqsanger" /> 137 <discover_datasets pattern="__designation_and_ext__" directory="out" format="fastqsanger" />
137 </collection> 138 </collection>
138 <collection type="list" name="output_collection_fasta" label="${tool.name} on ${on_string}"> 139 <collection type="list" name="output_collection_fasta" label="${tool.name} on ${on_string}">
139 <filter>out_format == 'fasta'</filter> 140 <filter>out_format == 'fasta'</filter>
141 <filter>demux_section['demux_options']['demux'] == 'yes'</filter>
140 <discover_datasets pattern="__designation_and_ext__" directory="out" format="fasta" /> 142 <discover_datasets pattern="__designation_and_ext__" directory="out" format="fasta" />
141 </collection> 143 </collection>
144 <data format="fastq" name="ouput_fastq">
145 <discover_datasets directory='out' pattern="(?P&lt;designation&gt;.+)" ext="fastq" visible="true" assign_primary_output="true" />
146 <filter>out_format == 'fastq'</filter>
147 <filter>demux_section['demux_options']['demux'] == 'no'</filter>
148 </data>
149 <data format="fasta" name="ouput_fasta">
150 <discover_datasets directory='out' pattern="(?P&lt;designation&gt;.+)" ext="fasta" visible="true" assign_primary_output="true" />
151 <filter>out_format == 'fasta'</filter>
152 <filter>demux_section['demux_options']['demux'] == 'no'</filter>
153 </data>
142 154
143 <data format="tabular" name="result_table" label="${tool.name} on ${on_string} (summary)" /> 155 <data format="tabular" name="result_table" label="${tool.name} on ${on_string} (summary)" />
144 </outputs> 156 </outputs>
145 157
146 <!-- ***************************************************************** --> 158 <!-- ***************************************************************** -->
175 <output_collection name="output_collection_fastq" type="list" count="3"> 187 <output_collection name="output_collection_fastq" type="list" count="3">
176 <element name="BC01" file="bar1_trim/BC01.fastq" compare="diff" decompress="true"/> 188 <element name="BC01" file="bar1_trim/BC01.fastq" compare="diff" decompress="true"/>
177 <element name="BC02" file="bar1_trim/BC02.fastq" compare="diff" decompress="true"/> 189 <element name="BC02" file="bar1_trim/BC02.fastq" compare="diff" decompress="true"/>
178 <element name="BC03" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/> 190 <element name="BC03" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/>
179 </output_collection> 191 </output_collection>
192 </test>
193 <test>
194 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
195 <param name="demux" value="no" />
196 <param name="trim" value="yes" />
197 <param name="out_format" value="fasta" />
198 <output name="output_fasta" file="no_demux.fasta" compare="diff" />
180 </test> 199 </test>
181 </tests> 200 </tests>
182 201
183 <!-- ***************************************************************** --> 202 <!-- ***************************************************************** -->
184 203