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comparison read_group_macros.xml @ 7:4f92dccc808a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:04:23 -0500
parents e23b0cdeeba6
children
comparison
equal deleted inserted replaced
6:e23b0cdeeba6 7:4f92dccc808a
119 #set $rg_pg = str($rg_param("PG")) 119 #set $rg_pg = str($rg_param("PG"))
120 #else 120 #else
121 #set $rg_pg = '' 121 #set $rg_pg = ''
122 #end if 122 #end if
123 123
124 #if str($rg_param("PI")) 124 #if $rg_param("PI") != None
125 #set $rg_pi = str($rg_param("PI")) 125 #set $rg_pi = str($rg_param("PI"))
126 #else 126 #else
127 #set $rg_pi = '' 127 #set $rg_pi = ''
128 #end if 128 #end if
129 129
144 <when value="false"> 144 <when value="false">
145 <yield /> 145 <yield />
146 </when> 146 </when>
147 </xml> 147 </xml>
148 <xml name="read_group_id_param"> 148 <xml name="read_group_id_param">
149 <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false"> 149 <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false">
150 <validator type="empty_field" /> 150 <validator type="empty_field" />
151 </param> 151 </param>
152 </xml> 152 </xml>
153 <xml name="read_group_id_conditional"> 153 <xml name="read_group_id_conditional">
154 <conditional name="read_group_id_conditional"> 154 <conditional name="read_group_id_conditional">
156 <expand macro="read_group_id_param" /> 156 <expand macro="read_group_id_param" />
157 </expand> 157 </expand>
158 </conditional> 158 </conditional>
159 </xml> 159 </xml>
160 <xml name="read_group_sm_param"> 160 <xml name="read_group_sm_param">
161 <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" /> 161 <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
162 </xml> 162 </xml>
163 <xml name="read_group_sm_conditional"> 163 <xml name="read_group_sm_conditional">
164 <conditional name="read_group_sm_conditional"> 164 <conditional name="read_group_sm_conditional">
165 <expand macro="read_group_auto_name_conditional"> 165 <expand macro="read_group_auto_name_conditional">
166 <expand macro="read_group_sm_param" /> 166 <expand macro="read_group_sm_param" />
169 </xml> 169 </xml>
170 <!-- Above SM param is optional (for SAM/BAM spec, this is required 170 <!-- Above SM param is optional (for SAM/BAM spec, this is required
171 as per Picard. 171 as per Picard.
172 --> 172 -->
173 <xml name="read_group_sm_param_required"> 173 <xml name="read_group_sm_param_required">
174 <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced"> 174 <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced">
175 <validator type="empty_field" /> 175 <validator type="empty_field" />
176 </param> 176 </param>
177 </xml> 177 </xml>
178 <xml name="read_group_sm_required_conditional"> 178 <xml name="read_group_sm_required_conditional">
179 <conditional name="read_group_sm_conditional"> 179 <conditional name="read_group_sm_conditional">
192 <option value="IONTORRENT">IONTORRENT</option> 192 <option value="IONTORRENT">IONTORRENT</option>
193 <option value="PACBIO">PACBIO</option> 193 <option value="PACBIO">PACBIO</option>
194 </param> 194 </param>
195 </xml> 195 </xml>
196 <xml name="read_group_lb_param"> 196 <xml name="read_group_lb_param">
197 <param name="LB" type="text" size="25" label="Library name (LB)" optional="true" /> 197 <param name="LB" type="text" label="Library name (LB)" optional="true" />
198 </xml> 198 </xml>
199 <xml name="read_group_lb_conditional"> 199 <xml name="read_group_lb_conditional">
200 <conditional name="read_group_lb_conditional"> 200 <conditional name="read_group_lb_conditional">
201 <expand macro="read_group_auto_name_conditional"> 201 <expand macro="read_group_auto_name_conditional">
202 <expand macro="read_group_lb_param" /> 202 <expand macro="read_group_lb_param" />
203 </expand> 203 </expand>
204 </conditional> 204 </conditional>
205 </xml> 205 </xml>
206 <xml name="read_group_lb_required_param"> 206 <xml name="read_group_lb_required_param">
207 <param name="LB" type="text" size="25" label="Library name (LB)" optional="false"> 207 <param name="LB" type="text" label="Library name (LB)" optional="false">
208 <validator type="empty_field" /> 208 <validator type="empty_field" />
209 </param> 209 </param>
210 </xml> 210 </xml>
211 <xml name="read_group_lb_required_conditional"> 211 <xml name="read_group_lb_required_conditional">
212 <conditional name="read_group_lb_conditional"> 212 <conditional name="read_group_lb_conditional">
214 <expand macro="read_group_lb_required_param" /> 214 <expand macro="read_group_lb_required_param" />
215 </expand> 215 </expand>
216 </conditional> 216 </conditional>
217 </xml> 217 </xml>
218 <xml name="read_group_cn_param"> 218 <xml name="read_group_cn_param">
219 <param name="CN" type="text" size="25" label="Sequencing center that produced the read (CN)" /> 219 <param name="CN" type="text" label="Sequencing center that produced the read (CN)" />
220 </xml> 220 </xml>
221 <xml name="read_group_ds_param"> 221 <xml name="read_group_ds_param">
222 <param name="DS" type="text" size="25" label="Description (DS)" /> 222 <param name="DS" type="text" label="Description (DS)" />
223 </xml> 223 </xml>
224 <xml name="read_group_dt_param"> 224 <xml name="read_group_dt_param">
225 <param name="DT" type="text" size="25" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" /> 225 <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
226 </xml> 226 </xml>
227 <xml name="read_group_fo_param"> 227 <xml name="read_group_fo_param">
228 <param name="FO" type="text" size="25" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/"> 228 <param name="FO" type="text" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
229 <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator> 229 <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator>
230 </param> 230 </param>
231 </xml> 231 </xml>
232 <xml name="read_group_ks_param"> 232 <xml name="read_group_ks_param">
233 <param name="KS" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" /> 233 <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
234 </xml> 234 </xml>
235 <xml name="read_group_pg_param"> 235 <xml name="read_group_pg_param">
236 <param name="PG" type="text" size="25" label="Programs used for processing the read group (PG)" /> 236 <param name="PG" type="text" label="Programs used for processing the read group (PG)" />
237 </xml> 237 </xml>
238 <xml name="read_group_pi_param"> 238 <xml name="read_group_pi_param">
239 <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" /> 239 <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />
240 </xml> 240 </xml>
241 <xml name="read_group_pu_param"> 241 <xml name="read_group_pu_param">
242 <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" /> 242 <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
243 </xml> 243 </xml>
244 <xml name="read_group_pu_required_param"> 244 <xml name="read_group_pu_required_param">
245 <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> 245 <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
246 </xml> 246 </xml>
247 <!-- Only ID is required - all groups available --> 247 <!-- Only ID is required - all groups available -->
248 <xml name="read_group_inputs_spec"> 248 <xml name="read_group_inputs_spec">
249 <expand macro="read_group_id_conditional" /> 249 <expand macro="read_group_id_conditional" />
250 <expand macro="read_group_sm_conditional" /> 250 <expand macro="read_group_sm_conditional" />