Mercurial > repos > iuc > stacks_procrad

comparison stacks_procrad.xml @ 3:11642e18f2b0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author iuc
date Sat, 25 Jun 2016 17:29:23 -0400
parents 6f9e8593e571
children c2733bcc51f7
comparison
equal deleted inserted replaced
2:5d12647ff71f 3:11642e18f2b0
1 <tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.1"> 1 <tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.2">
2 <description>the Stacks demultiplexing script</description> 2 <description>the Stacks demultiplexing script</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
147 147
148 <outputs> 148 <outputs>
149 <data format="txt" name="output_log" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" from_work_dir="stacks_outputs/process_radtags.log" /> 149 <data format="txt" name="output_log" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" from_work_dir="stacks_outputs/process_radtags.log" />
150 150
151 <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}"> 151 <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}">
152 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq" ext="fastqsanger" directory="stacks_outputs" /> 152 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
153 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fa" ext="fasta" directory="stacks_outputs" /> 153 <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
154 </collection> 154 </collection>
155 <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}"> 155 <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}">
156 <filter>input_type['options_type_selector'] == "paired"</filter> 156 <filter>input_type['options_type_selector'] == "paired"</filter>
157 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq" ext="fastqsanger" directory="stacks_outputs" /> 157 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
158 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fa" ext="fasta" directory="stacks_outputs" /> 158 <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
159 </collection> 159 </collection>
160 <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}"> 160 <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}">
161 <filter>capture is True</filter> 161 <filter>capture is True</filter>
162 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.discards" ext="fastqsanger" directory="stacks_outputs" /> 162 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" />
163 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa\.discards" ext="fasta" directory="stacks_outputs" /> 163 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" />
164 </collection> 164 </collection>
165 </outputs> 165 </outputs>
166 166
167 <tests> 167 <tests>
168 <test> 168 <test>