Mercurial > repos > devteam > bowtie2

comparison bowtie2_macros.xml @ 33:c3d19e7ee879 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
author iuc
date Wed, 24 Sep 2025 13:36:57 +0000
parents 6b4916819621
children
comparison
equal deleted inserted replaced
32:6b4916819621 33:c3d19e7ee879
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">2.5.0</token> 2 <token name="@TOOL_VERSION@">2.5.4</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">23.0</token>
4 <!-- Import this at the top of your command block and then 5 <!-- Import this at the top of your command block and then
5 define rg_auto_name. --> 6 define rg_auto_name. -->
6 <token name="@define_read_group_helpers@"> 7 <token name="@define_read_group_helpers@">
7 #def identifier_or_name($input1) 8 #def identifier_or_name($input1)
8 #if hasattr($input1, 'element_identifier') 9 #if hasattr($input1, 'element_identifier')
57 --> 58 -->
58 <token name="@set_read_group_vars@"> 59 <token name="@set_read_group_vars@">
59 #if $use_rg 60 #if $use_rg
60 #if $rg_param('read_group_id_conditional') is None 61 #if $rg_param('read_group_id_conditional') is None
61 #set $rg_id = $rg_auto_name 62 #set $rg_id = $rg_auto_name
62 #elif $rg_param('read_group_id_conditional').do_auto_name 63 #elif $rg_param('read_group_id_conditional').do_auto_name == "yes"
63 #set $rg_id = $rg_auto_name 64 #set $rg_id = $rg_auto_name
64 #else 65 #else
65 #set $rg_id = str($rg_param('read_group_id_conditional').ID) 66 #set $rg_id = str($rg_param('read_group_id_conditional').ID)
66 #end if 67 #end if
67 68
68 #if $rg_param('read_group_sm_conditional') is None 69 #if $rg_param('read_group_sm_conditional') is None
69 #set $rg_sm = '' 70 #set $rg_sm = ''
70 #elif $rg_param('read_group_sm_conditional').do_auto_name 71 #elif $rg_param('read_group_sm_conditional').do_auto_name == "yes"
71 #set $rg_sm = $rg_auto_name 72 #set $rg_sm = $rg_auto_name
72 #else 73 #else
73 #set $rg_sm = str($rg_param('read_group_sm_conditional').SM) 74 #set $rg_sm = str($rg_param('read_group_sm_conditional').SM)
74 #end if 75 #end if
75 76
79 #set $rg_pl = '' 80 #set $rg_pl = ''
80 #end if 81 #end if
81 82
82 #if $rg_param('read_group_lb_conditional') is None 83 #if $rg_param('read_group_lb_conditional') is None
83 #set $rg_lb = '' 84 #set $rg_lb = ''
84 #elif $rg_param('read_group_lb_conditional').do_auto_name 85 #elif $rg_param('read_group_lb_conditional').do_auto_name == "yes"
85 #set $rg_lb = $rg_auto_name 86 #set $rg_lb = $rg_auto_name
86 #else 87 #else
87 #set $rg_lb = str($rg_param('read_group_lb_conditional').LB) 88 #set $rg_lb = str($rg_param('read_group_lb_conditional').LB)
88 #end if 89 #end if
89 90
138 </token> 139 </token>
139 <token name="@set_use_rg_var@"> 140 <token name="@set_use_rg_var@">
140 #set $use_rg = str($rg.rg_selector) != "do_not_set" 141 #set $use_rg = str($rg.rg_selector) != "do_not_set"
141 </token> 142 </token>
142 <xml name="read_group_auto_name_conditional"> 143 <xml name="read_group_auto_name_conditional">
143 <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="false" /> 144 <param name="do_auto_name" type="select" optional="false" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value">
144 <when value="true"> 145 <option value="yes">Yes</option>
145 </when> 146 <option value="no" selected="true">No</option>
146 <when value="false"> 147 </param>
148 <when value="yes"/>
149 <when value="no">
147 <yield /> 150 <yield />
148 </when> 151 </when>
149 </xml> 152 </xml>
150 <xml name="read_group_id_param"> 153 <xml name="read_group_id_param">
151 <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"> 154 <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment">
152 <validator type="empty_field" /> 155 <validator type="empty_field" />
153 </param> 156 </param>
154 </xml> 157 </xml>
155 <xml name="read_group_id_conditional"> 158 <xml name="read_group_id_conditional">
156 <conditional name="read_group_id_conditional"> 159 <conditional name="read_group_id_conditional">
171 </xml> 174 </xml>
172 <!-- Above SM param is optional (for SAM/BAM spec, this is required 175 <!-- Above SM param is optional (for SAM/BAM spec, this is required
173 as per Picard. 176 as per Picard.
174 --> 177 -->
175 <xml name="read_group_sm_param_required"> 178 <xml name="read_group_sm_param_required">
176 <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"> 179 <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">
177 <validator type="empty_field" /> 180 <validator type="empty_field" />
178 </param> 181 </param>
179 </xml> 182 </xml>
180 <xml name="read_group_sm_required_conditional"> 183 <xml name="read_group_sm_required_conditional">
181 <conditional name="read_group_sm_conditional"> 184 <conditional name="read_group_sm_conditional">
194 <option value="IONTORRENT">IONTORRENT</option> 197 <option value="IONTORRENT">IONTORRENT</option>
195 <option value="PACBIO">PACBIO</option> 198 <option value="PACBIO">PACBIO</option>
196 </param> 199 </param>
197 </xml> 200 </xml>
198 <xml name="read_group_lb_param"> 201 <xml name="read_group_lb_param">
199 <param name="LB" type="text" label="Library name (LB)" optional="true" /> 202 <param name="LB" type="text" label="Library name (LB)"/>
200 </xml> 203 </xml>
201 <xml name="read_group_lb_conditional"> 204 <xml name="read_group_lb_conditional">
202 <conditional name="read_group_lb_conditional"> 205 <conditional name="read_group_lb_conditional">
203 <expand macro="read_group_auto_name_conditional"> 206 <expand macro="read_group_auto_name_conditional">
204 <expand macro="read_group_lb_param" /> 207 <expand macro="read_group_lb_param" />
205 </expand> 208 </expand>
206 </conditional> 209 </conditional>
207 </xml> 210 </xml>
208 <xml name="read_group_lb_required_param"> 211 <xml name="read_group_lb_required_param">
209 <param name="LB" type="text" label="Library name (LB)" optional="false"> 212 <param name="LB" type="text" label="Library name (LB)">
210 <validator type="empty_field" /> 213 <validator type="empty_field" />
211 </param> 214 </param>
212 </xml> 215 </xml>
213 <xml name="read_group_lb_required_conditional"> 216 <xml name="read_group_lb_required_conditional">
214 <conditional name="read_group_lb_conditional"> 217 <conditional name="read_group_lb_conditional">
225 </xml> 228 </xml>
226 <xml name="read_group_dt_param"> 229 <xml name="read_group_dt_param">
227 <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" /> 230 <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
228 </xml> 231 </xml>
229 <xml name="read_group_fo_param"> 232 <xml name="read_group_fo_param">
230 <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]+/"> 233 <param name="FO" type="text" 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]+/">
231 <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator> 234 <validator type="regex" message="Invalid flow order">|\*|[ACMGRSVTWYHKDBN]+$</validator>
232 </param> 235 </param>
233 </xml> 236 </xml>
234 <xml name="read_group_ks_param"> 237 <xml name="read_group_ks_param">
235 <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" /> 238 <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
236 </xml> 239 </xml>
239 </xml> 242 </xml>
240 <xml name="read_group_pi_param"> 243 <xml name="read_group_pi_param">
241 <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" /> 244 <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />
242 </xml> 245 </xml>
243 <xml name="read_group_pu_param"> 246 <xml name="read_group_pu_param">
244 <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" /> 247 <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" />
245 </xml> 248 </xml>
246 <xml name="read_group_pu_required_param"> 249 <xml name="read_group_pu_required_param">
247 <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" /> 250 <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" />
248 </xml> 251 </xml>
249 <!-- Only ID is required - all groups available --> 252 <!-- Only ID is required - all groups available -->
250 <xml name="read_group_inputs_spec"> 253 <xml name="read_group_inputs_spec">
251 <expand macro="read_group_id_conditional" /> 254 <expand macro="read_group_id_conditional" />
252 <expand macro="read_group_sm_conditional" /> 255 <expand macro="read_group_sm_conditional" />
285 <expand macro="read_group_inputs_picard" /> 288 <expand macro="read_group_inputs_picard" />
286 </when> 289 </when>
287 <when value="set"> 290 <when value="set">
288 <expand macro="read_group_inputs_spec" /> 291 <expand macro="read_group_inputs_spec" />
289 </when> 292 </when>
290 <when value="set_id_auto"> 293 <when value="set_id_auto"/>
291 </when> 294 <when value="do_not_set"/>
292 <when value="do_not_set">
293 </when>
294 </conditional> 295 </conditional>
295 </xml> 296 </xml>
296 <xml name="paired_end_options"> 297 <xml name="paired_end_options">
297 <conditional name="paired_options"> 298 <conditional name="paired_options">
298 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information"> 299 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
308 help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)"> 309 help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)">
309 <option value="--fr" selected="True">--fr</option> 310 <option value="--fr" selected="True">--fr</option>
310 <option value="--rf">--rf</option> 311 <option value="--rf">--rf</option>
311 <option value="--ff">--ff</option> 312 <option value="--ff">--ff</option>
312 </param> 313 </param>
313 <param argument="--no-mixed" name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/> 314 <param argument="--no-mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
314 <param argument="--no-discordant" name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/> 315 <param argument="--no-discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
315 <param argument="--dovetail" name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/> 316 <param argument="--dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
316 <param argument="--no-contain" name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/> 317 <param argument="--no-contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
317 <param argument="--no-overlap" name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/> 318 <param argument="--no-overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
318 </when> 319 </when>
319 <when value="no"> 320 <when value="no">
320 <!-- do nothing --> 321 <!-- do nothing -->
321 </when> 322 </when>
322 </conditional> 323 </conditional>