Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna
comparison bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.xml @ 5:b300c15426f5 draft
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author | jackcurragh |
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date | Mon, 21 Mar 2022 12:53:51 +0000 |
parents | 01ca7075c109 |
children | d3c89fb66c4d |
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4:01ca7075c109 | 5:b300c15426f5 |
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1 <tool id="bowtie_remove_rrna_wrapper" name="Remove rRNA using Bowtie" version="1.3"> | 1 <tool id="bowtie_rRNA_removal_wrapper" name="Remove rRNA using Bowtie" version="1.4.0"> |
2 <description></description> | 2 <description></description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.2.0">bowtie</requirement> | 4 <requirement type="package" version="1.2.0">bowtie</requirement> |
5 </requirements> | 5 </requirements> |
6 <version_command>bowtie --version</version_command> | 6 <version_command>bowtie --version</version_command> |
154 </command> | 154 </command> |
155 <inputs> | 155 <inputs> |
156 <conditional name="refGenomeSource"> | 156 <conditional name="refGenomeSource"> |
157 <param name="genomeSource" 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"> | 157 <param name="genomeSource" 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"> |
158 <option value="indexed">Use a built-in index</option> | 158 <option value="indexed">Use a built-in index</option> |
159 <option value="history">Use one from the history</option> | 159 <option value="history" selected="True">Use one from the history</option> |
160 </param> | 160 </param> |
161 <when value="indexed"> | 161 <when value="indexed"> |
162 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> | 162 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> |
163 <options from_data_table="bowtie_indexes"> | 163 <options from_data_table="bowtie_indexes"> |
164 <filter type="sort_by" column="2" /> | 164 <filter type="sort_by" column="2" /> |
246 <option value="noRound">Do not round to nearest 10</option> | 246 <option value="noRound">Do not round to nearest 10</option> |
247 </param> | 247 </param> |
248 </when> | 248 </when> |
249 <when value="vMode"> | 249 <when value="vMode"> |
250 <param name="maxMismatches" type="integer" value="3" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" /> | 250 <param name="maxMismatches" type="integer" value="3" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" /> |
251 <param name="sSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" /> | |
251 </when> | 252 </when> |
252 </conditional> | 253 </conditional> |
253 <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)"> | 254 <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)"> |
254 <option value="forward">Align against the forward reference strand</option> | 255 <option value="forward">Align against the forward reference strand</option> |
255 <option value="noForward">Do not align against the forward reference strand</option> | 256 <option value="noForward">Do not align against the forward reference strand</option> |
256 </param> | 257 </param> |
257 <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)"> | 258 <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)"> |
258 <option value="reverse">Align against the reverse-complement reference strand</option> | 259 <option value="reverse">Align against the reverse-complement reference strand</option> |
259 <option value="noReverse">Do not align against the reverse-complement reference strand</option> | 260 <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option> |
260 </param> | 261 </param> |
261 <conditional name="sBestOption"> | 262 <conditional name="sBestOption"> |
262 <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> | 263 <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> |
263 <option value="noBest">Do not use best</option> | 264 <option value="noBest">Do not use best</option> |
264 <option value="doBest">Use best</option> | 265 <option value="doBest">Use best</option> |
293 </when> | 294 </when> |
294 </conditional> <!-- bestOption --> | 295 </conditional> <!-- bestOption --> |
295 <conditional name="sAllValAlignsOption"> | 296 <conditional name="sAllValAlignsOption"> |
296 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> | 297 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> |
297 <option value="noAllValAligns">Do not report all valid alignments</option> | 298 <option value="noAllValAligns">Do not report all valid alignments</option> |
298 <option value="doAllValAligns">Report all valid alignments</option> | 299 <option value="doAllValAligns" selected="true">Report all valid alignments</option> |
299 </param> | 300 </param> |
300 <when value="noAllValAligns"> | 301 <when value="noAllValAligns"> |
301 <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" /> | 302 <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" /> |
302 </when> | 303 </when> |
303 <when value="doAllValAligns" /> | 304 <when value="doAllValAligns" /> |
304 </conditional> | 305 </conditional> |
305 <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" /> | 306 <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" /> |
306 <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" /> | 307 <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" /> |
307 <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" /> | 308 <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Write all reads that could not be aligned to a file (--un)" /> |
308 <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> | 309 <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> |
309 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> | 310 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> |
310 </when> <!-- full --> | 311 </when> <!-- full --> |
311 </conditional> <!-- sParams --> | 312 </conditional> <!-- sParams --> |
312 </when> <!-- single --> | 313 </when> <!-- single --> |
337 <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> | 338 <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> |
338 <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> | 339 <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> |
339 <conditional name="alignModeOption"> | 340 <conditional name="alignModeOption"> |
340 <param name="alignMode" type="select" label="Alignment mode"> | 341 <param name="alignMode" type="select" label="Alignment mode"> |
341 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option> | 342 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option> |
342 <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option> | 343 <option value="vMode" selected="true">ignore qualities, limit end-to-end mismatches (-v)</option> |
343 </param> | 344 </param> |
344 <when value="nMode"> | 345 <when value="nMode"> |
345 <param name="pMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> | 346 <param name="pMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> |
346 <param name="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" /> | 347 <param name="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" /> |
347 <param name="pSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" /> | 348 <param name="pSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" /> |
350 <option value="noRound">Do not round to nearest 10</option> | 351 <option value="noRound">Do not round to nearest 10</option> |
351 </param> | 352 </param> |
352 </when> | 353 </when> |
353 <when value="vMode"> | 354 <when value="vMode"> |
354 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" /> | 355 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" /> |
356 <param name="pSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" /> | |
355 </when> | 357 </when> |
356 </conditional> | 358 </conditional> |
357 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" /> | 359 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" /> |
358 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)"> | 360 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)"> |
359 <option value="forward">Align against the forward reference strand</option> | 361 <option value="forward">Align against the forward reference strand</option> |
360 <option value="noForward">Do not align against the forward reference strand</option> | 362 <option value="noForward">Do not align against the forward reference strand</option> |
361 </param> | 363 </param> |
362 <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)"> | 364 <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)"> |
363 <option value="reverse">Align against the reverse-complement reference strand</option> | 365 <option value="reverse">Align against the reverse-complement reference strand</option> |
364 <option value="noReverse">Do not align against the reverse-complement reference strand</option> | 366 <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option> |
365 </param> | 367 </param> |
366 <conditional name="pBestOption"> | 368 <conditional name="pBestOption"> |
367 <param name="pBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> | 369 <param name="pBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> |
368 <option value="noBest">Do not use best</option> | 370 <option value="noBest">Do not use best</option> |
369 <option value="doBest">Use best</option> | 371 <option value="doBest">Use best</option> |
400 </when> | 402 </when> |
401 </conditional> | 403 </conditional> |
402 <conditional name="pAllValAlignsOption"> | 404 <conditional name="pAllValAlignsOption"> |
403 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)"> | 405 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)"> |
404 <option value="noAllValAligns">Do not report all valid alignments</option> | 406 <option value="noAllValAligns">Do not report all valid alignments</option> |
405 <option value="doAllValAligns">Report all valid alignments</option> | 407 <option value="doAllValAligns" selected="True">Report all valid alignments</option> |
406 </param> | 408 </param> |
407 <when value="noAllValAligns"> | 409 <when value="noAllValAligns"> |
408 <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" /> | 410 <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" /> |
409 </when> | 411 </when> |
410 <when value="doAllValAligns" /> | 412 <when value="doAllValAligns" /> |
416 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> | 418 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> |
417 </when> <!-- full --> | 419 </when> <!-- full --> |
418 </conditional> <!-- pParams --> | 420 </conditional> <!-- pParams --> |
419 </when> <!-- paired --> | 421 </when> <!-- paired --> |
420 </conditional> <!-- singlePaired --> | 422 </conditional> <!-- singlePaired --> |
421 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" /> | 423 <param name="save_mapping_stats" type="boolean" checked="True" label="Save the bowtie mapping statistics to the history" /> |
422 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" /> | 424 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" /> |
423 </inputs> | 425 </inputs> |
424 <outputs> | 426 <outputs> |
425 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> | 427 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> |
426 <actions> | 428 <actions> |