Mercurial > repos > big-tiandm > mirplant2

comparison miRPlant.xml @ 52:8b8c356e6db5 draft

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Uploaded
author big-tiandm
date Fri, 05 Dec 2014 01:28:46 -0500
parents 7b5a48b972e9
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51:3202911efdae 52:8b8c356e6db5
89 89
90 <conditional name="params"> 90 <conditional name="params">
91 <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)"> 91 <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)">
92 <option value="yes" selected="true">yes</option> 92 <option value="yes" selected="true">yes</option>
93 <option value="no">no</option> 93 <option value="no">no</option>
94 </param> 94 </param>
95 <when value="yes"> 95 <when value="yes">
96 <!--param name="rfam" type="data" label="rfam sequence file" /--> 96 <!--param name="rfam" type="data" label="rfam sequence file" /-->
97 <conditional name="reference_rfam"> 97 <conditional name="reference_rfam">
98 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> 98 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
99 <option value="indexed">Use a built-in index</option> 99 <option value="indexed">Use a built-in index</option>
112 </when> 112 </when>
113 </conditional> 113 </conditional>
114 114
115 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/> 115 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
116 116
117 <conditional name="rfamresult"> 117 <param name="delet_rfam" type="select" label="delet rfam mapped reads">
118 <param name="delet_rfam" type="select" label="delet rfam mapped reads"> 118 <option value="yes" selected="true">yes</option>
119 <option value="yes" selected="true">yes</option> 119 <option value="no">no</option>
120 <option value="no">no</option> 120 </param>
121 </param>
122 </conditional> <!-- params -->
123
124
125 </when> 121 </when>
126 </conditional> <!-- params --> 122 </conditional>
127 123
128 124
129 <!--param name="input" format="tabular" type="data" label="input config file" /-->
130 125
131 <param name="format" type="select" lable="raw data format" multiple="false"> 126 <param name="format" type="select" lable="raw data format" multiple="false">
132 <option value="fastq">Raw data is fastq. format</option> 127 <option value="fastq">Raw data is fastq. format</option>
133 <option value="fasta">Raw data is fasta. format</option> 128 <option value="fasta">Raw data is fasta. format</option>
134 </param> 129 </param>
136 <param name="phred" type="select" lable="input quals are Phred+64 or Phred+33" multiple="false"> 131 <param name="phred" type="select" lable="input quals are Phred+64 or Phred+33" multiple="false">
137 <option value="64">Phred+64</option> 132 <option value="64">Phred+64</option>
138 <option value="33" selected="true">Phred+33</option> 133 <option value="33" selected="true">Phred+33</option>
139 </param> 134 </param>
140 135
141 <conditional name="reference_genome">
142 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
143 <option value="indexed">Use a built-in index</option>
144 <option value="history">Use one from the history</option>
145 </param>
146 <when value="indexed">
147 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
148 <options from_data_table="bowtie_indexes">
149 <filter type="sort_by" column="2"/>
150 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
151 </options>
152 </param>
153 </when>
154 <when value="history">
155 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
156 </when>
157 </conditional>
158
159 <!--param type="data" name="index" label="genome sequence bowtie index"/-->
160 <conditional name="params">
161 <param name="known_microRNA" type="select" label="Analysis known microRNAs(eg. from mirbase)">
162 <option value="yes" selected="true">yes</option>
163 <option value="no">no</option>
164 </param>
165 <when value="yes">
166 <param name="mat" type="data" label="mature microRNA sequence file" />
167 <param name="pre" type="data" label="precursor microRNA sequence fie" />
168 </when>
169 </conditional> <!-- params -->
170
171 <conditional name="params">
172 <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)">
173 <option value="yes" selected="true">yes</option>
174 <option value="no">no</option>
175 </param>
176 <when value="yes">
177 <!--param name="rfam" type="data" label="rfam sequence file" /-->
178 <when value="yes">
179 <!--param name="rfam" type="data" label="rfam sequence file" /-->
180 <conditional name="reference_rfam">
181 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
182 <option value="indexed">Use a built-in index</option>
183 <option value="history">Use one from the history</option>
184 </param>
185 <when value="indexed">
186 <param name="index" type="select" label="Select a reference" help="If your reference of interest is not listed, contact the Galaxy team">
187 <options from_data_table="rfam_bowtie_indexes">
188 <filter type="sort_by" column="2"/>
189 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
190 </options>
191 </param>
192 </when>
193 <when value="history">
194 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference" />
195 </when>
196 </conditional>
197
198 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
199 </when>
200 </conditional> <!-- params -->
201
202 <!--param type="data" name="idx2" label="rfam sequence bowtie index " -->
203 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" /> 136 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
204 <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" /> 137 <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" />
205 <param name="min" type="integer" value="19" label="minimum microRNA length" /> 138 <param name="min" type="integer" value="19" label="minimum microRNA length" />
206 <param name="max" type="integer" value="28" label="maximum microRNA length" /> 139 <param name="max" type="integer" value="28" label="maximum microRNA length" />
207 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to precursors" /> 140 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to precursors" />