Mercurial > repos > jackcurragh > ribogalaxy_bowtie_transcriptome

comparison bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml @ 1:14fb4b4872e3 draft

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author jackcurragh
date Tue, 22 Mar 2022 12:34:36 +0000
parents 1b109d213a42
children cd79614871c2
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0:1b109d213a42 1:14fb4b4872e3
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>
7 <command> 7 <command>
8 python '$__tool_directory__/bowtie_wrapper.py' 8 python '$__tool_directory__/bowtie_transcriptome_wrapper.py'
9 ## Set number of threads 9 ## Set number of threads
10 --threads="\${GALAXY_SLOTS:-4}" 10 --threads="\${GALAXY_SLOTS:-4}"
11 ## Outputs 11 ## Outputs
12 --output="${output}" 12 --output="${output}"
13 #if str( $singlePaired.sPaired ) == "single" 13 #if str( $singlePaired.sPaired ) == "single"
152 --output_mapping_stats="$mapping_stats" 152 --output_mapping_stats="$mapping_stats"
153 #end if 153 #end if
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 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">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" help="if your reference of interest is not listed - contact RiboGalaxy 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" />
165 <validator type="no_options" message="No indexes are available" /> 165 <validator type="no_options" message="No indexes are available" />
166 </options> 166 </options>
167 </param> 167 </param>
168 </when> 168 </when>
169 <when value="history"> 169 <when value="history">
170 <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" /> 170 <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference" />
171 <conditional name="indexParams"> 171 <conditional name="indexParams">
172 <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index"> 172 <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index">
173 <option value="indexPreSet">Default</option> 173 <option value="indexPreSet">Default</option>
174 <option value="indexFull">Set your own</option> 174 <option value="indexFull">Set your own</option>
175 </param> 175 </param>
255 <option value="forward">Align against the forward reference strand</option> 255 <option value="forward">Align against the forward reference strand</option>
256 <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>
257 </param> 257 </param>
258 <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)">
259 <option value="reverse">Align against the reverse-complement reference strand</option> 259 <option value="reverse">Align against the reverse-complement reference strand</option>
260 <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>
261 </param> 261 </param>
262 <conditional name="sBestOption"> 262 <conditional name="sBestOption">
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 <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">
264 <option value="noBest">Do not use best</option> 264 <option value="noBest">Do not use best</option>
265 <option value="doBest">Use best</option> 265 <option value="doBest">Use best</option>
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="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
339 <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)" />
340 <conditional name="alignModeOption"> 340 <conditional name="alignModeOption">
341 <param name="alignMode" type="select" label="Alignment mode"> 341 <param name="alignMode" type="select" label="Alignment mode">
342 <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>
343 <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>
344 </param> 344 </param>
345 <when value="nMode"> 345 <when value="nMode">
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="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" />
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="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
348 <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" />
351 <option value="noRound">Do not round to nearest 10</option> 351 <option value="noRound">Do not round to nearest 10</option>
352 </param> 352 </param>
353 </when> 353 </when>
354 <when value="vMode"> 354 <when value="vMode">
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" /> 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" />
356 </when> 357 </when>
357 </conditional> 358 </conditional>
358 <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)" />
359 <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)">
360 <option value="forward">Align against the forward reference strand</option> 361 <option value="forward">Align against the forward reference strand</option>