Mercurial > repos > wolma > mimodd_core
comparison reheader.xml @ 1:1425ea794026 draft default tip
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864
| author | wolma |
|---|---|
| date | Mon, 18 Dec 2017 03:39:07 -0500 |
| parents | aa82b2e54055 |
| children |
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| 0:aa82b2e54055 | 1:1425ea794026 |
|---|---|
| 27 <repeat name="rg" title="new read-group info" default="1" min="1"> | 27 <repeat name="rg" title="new read-group info" default="1" min="1"> |
| 28 <param name="source_id" type="text" | 28 <param name="source_id" type="text" |
| 29 label="read-group ID (will create the read-group if it does not exist)" | 29 label="read-group ID (will create the read-group if it does not exist)" |
| 30 help="required field"> | 30 help="required field"> |
| 31 <validator type="empty_field" /> | 31 <validator type="empty_field" /> |
| 32 <expand macro="lex_sam_header" /> | |
| 32 </param> | 33 </param> |
| 33 <param name="rg_id" type="hidden" value="" /> | 34 <param name="rg_id" type="hidden" value="" /> |
| 34 <param name="rg_sm" type="text" label="sample name" | 35 <param name="rg_sm" type="text" label="sample name" |
| 35 help="required field"> | 36 help="required field"> |
| 36 <validator type="empty_field" /> | 37 <validator type="empty_field" /> |
| 37 </param> | 38 <expand macro="lex_sam_header" /> |
| 38 <param name="rg_ds" type="text" label="description" /> | 39 </param> |
| 40 <param name="rg_ds" type="text" label="description"> | |
| 41 <expand macro="lex_sam_header" /> | |
| 42 </param> | |
| 39 <param name="rg_date" type="text" | 43 <param name="rg_date" type="text" |
| 40 label="date (YY-MM-DD format) the run was produced" /> | 44 label="date (YY-MM-DD format) the run was produced"> |
| 45 <expand macro="YYYY-MM-DD_format_validator" /> | |
| 46 </param> | |
| 41 <param name="rg_cn" type="text" | 47 <param name="rg_cn" type="text" |
| 42 label="name of sequencing center" /> | 48 label="name of sequencing center"> |
| 43 <param name="rg_lb" type="text" label="read-group library" /> | 49 <expand macro="lex_sam_header" /> |
| 50 </param> | |
| 51 <param name="rg_lb" type="text" label="read-group library"> | |
| 52 <expand macro="lex_sam_header" /> | |
| 53 </param> | |
| 44 <param name="rg_pl" type="text" | 54 <param name="rg_pl" type="text" |
| 45 label="platform/technology used to produce the reads" /> | 55 label="platform/technology used to produce the reads"> |
| 56 <expand macro="known_sequencing_platform options" /> | |
| 57 <expand macro="lex_sam_header" /> | |
| 58 </param> | |
| 46 <param name="rg_pi" type="text" | 59 <param name="rg_pi" type="text" |
| 47 label="predicted median insert size" /> | 60 label="predicted median insert size"> |
| 61 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> | |
| 62 </param> | |
| 48 <param name="rg_pu" type="text" | 63 <param name="rg_pu" type="text" |
| 49 label="platform unit; unique identifier" /> | 64 label="platform unit; unique identifier"> |
| 65 <expand macro="lex_sam_header" /> | |
| 66 </param> | |
| 50 </repeat> | 67 </repeat> |
| 51 </when> | 68 </when> |
| 52 </conditional> | 69 </conditional> |
| 53 </macro> | 70 </macro> |
| 54 </macros> | 71 </macros> |
| 178 <option value="update">Yes, append new comments to existing ones</option> | 195 <option value="update">Yes, append new comments to existing ones</option> |
| 179 <option value="replace">Yes, replace all existing comments</option> | 196 <option value="replace">Yes, replace all existing comments</option> |
| 180 </param> | 197 </param> |
| 181 <when value="update"> | 198 <when value="update"> |
| 182 <repeat name="coinfo" title="comment line" default="0" min="0"> | 199 <repeat name="coinfo" title="comment line" default="0" min="0"> |
| 183 <param name="line" type="text" size="80" /> | 200 <param name="line" type="text" size="80"> |
| 201 <expand macro="lex_sam_header" /> | |
| 202 </param> | |
| 184 </repeat> | 203 </repeat> |
| 185 </when> | 204 </when> |
| 186 <when value="replace"> | 205 <when value="replace"> |
| 187 <repeat name="coinfo" title="comment line" default="0" min="0"> | 206 <repeat name="coinfo" title="comment line" default="0" min="0"> |
| 188 <param name="line" type="text" size="80" /> | 207 <param name="line" type="text" size="80"> |
| 208 <expand macro="lex_sam_header" /> | |
| 209 </param> | |
| 189 </repeat> | 210 </repeat> |
| 190 </when> | 211 </when> |
| 191 <when value="ignore"> | 212 <when value="ignore"> |
| 192 </when> | 213 </when> |
| 193 </conditional> | 214 </conditional> |
| 194 <repeat name="rg_renaming" title="rename read-group" default="0" min="0" | 215 <repeat name="rg_renaming" title="rename read-group" default="0" min="0" |
| 195 help="Warning: changing read-group IDs may increase job runtime substantially."> | 216 help="Warning: changing read-group IDs may increase job runtime substantially."> |
| 196 <param name="from" type="text" size="30" label="old name" | 217 <param name="from" type="text" size="30" label="old name" |
| 197 help="as it appears in the current input file header"/> | 218 help="as it appears in the current input file header"> |
| 198 <param name="to" type="text" size="30" label="new name" /> | 219 <expand macro="lex_sam_header" /> |
| 220 </param> | |
| 221 <param name="to" type="text" size="30" label="new name"> | |
| 222 <expand macro="lex_sam_header" /> | |
| 223 </param> | |
| 199 </repeat> | 224 </repeat> |
| 200 <repeat name="sq_renaming" title="rename sequence" default="0" min="0" | 225 <repeat name="sq_renaming" title="rename sequence" default="0" min="0" |
| 201 help="Warning: changing sequence names may increase job runtime substantially."> | 226 help="Warning: changing sequence names may increase job runtime substantially."> |
| 202 <param name="from" type="text" size="30" label="old name" | 227 <param name="from" type="text" size="30" label="old name" |
| 203 help="as it appears in the current input file header"/> | 228 help="as it appears in the current input file header"> |
| 204 <param name="to" type="text" size="30" label="new name" /> | 229 <expand macro="lex_sam_header" /> |
| 230 </param> | |
| 231 <param name="to" type="text" size="30" label="new name"> | |
| 232 <validator type="expression" message="Sequence names may not contain non-ASCII, whitespace, non-printable characters, nor any of: <>[]*;=,">all((32 < ord(c) < 127 and c not in '<>[]*;=,') for c in value)</validator> | |
| 233 <expand macro="lex_sam_header" /> | |
| 234 </param> | |
| 205 </repeat> | 235 </repeat> |
| 206 </inputs> | 236 </inputs> |
| 207 | 237 |
| 208 <outputs> | 238 <outputs> |
| 209 <data name="output" format="bam" | 239 <data name="output" format="bam" |