Mercurial > repos > iuc > data_manager_star_index_builder
comparison data_manager/macros.xml @ 9:c520a52b5174 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
author | iuc |
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date | Fri, 10 Sep 2021 16:44:59 +0000 |
parents | 6c6c6df09e64 |
children | a225487bf618 |
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8:d3879aceba04 | 9:c520a52b5174 |
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3 whenever you make changes to the following two version tokens! | 3 whenever you make changes to the following two version tokens! |
4 The data manager uses a symlink to this macro file to keep the STAR and | 4 The data manager uses a symlink to this macro file to keep the STAR and |
5 the index versions in sync, but you should manually adjust the +galaxy | 5 the index versions in sync, but you should manually adjust the +galaxy |
6 version number. --> | 6 version number. --> |
7 <!-- STAR version to be used --> | 7 <!-- STAR version to be used --> |
8 <token name="@VERSION@">2.7.5b</token> | 8 <token name="@VERSION@">2.7.8a</token> |
9 <!-- STAR index version compatible with this version of STAR | 9 <!-- STAR index version compatible with this version of STAR |
10 This is the STAR version that introduced the index structure expected | 10 This is the STAR version that introduced the index structure expected |
11 by the current version. | 11 by the current version. |
12 It can be found for any specific version of STAR with: | 12 It can be found for any specific version of STAR with: |
13 STAR -h | grep versionGenome | 13 STAR -h | grep versionGenome |
20 <requirements> | 20 <requirements> |
21 <requirement type="package" version="@VERSION@">star</requirement> | 21 <requirement type="package" version="@VERSION@">star</requirement> |
22 <requirement type="package" version="1.9">samtools</requirement> | 22 <requirement type="package" version="1.9">samtools</requirement> |
23 <yield /> | 23 <yield /> |
24 </requirements> | 24 </requirements> |
25 </xml> | |
26 | |
27 <xml name="edam"> | |
28 <edam_topics> | |
29 <edam_topic>topic_3170</edam_topic> | |
30 <edam_topic>topic_3308</edam_topic> | |
31 </edam_topics> | |
32 <edam_operations> | |
33 <edam_operation>operation_0292</edam_operation> | |
34 </edam_operations> | |
25 </xml> | 35 </xml> |
26 | 36 |
27 <xml name="index_selection" token_with_gene_model="0"> | 37 <xml name="index_selection" token_with_gene_model="0"> |
28 <param argument="--genomeDir" name="genomeDir" type="select" | 38 <param argument="--genomeDir" name="genomeDir" type="select" |
29 label="Select reference genome" | 39 label="Select reference genome" |
120 #end if | 130 #end if |
121 #end if | 131 #end if |
122 #end if | 132 #end if |
123 #end if | 133 #end if |
124 ]]></token> | 134 ]]></token> |
135 <token name="@READSHANDLING@" ><![CDATA[ | |
136 ## Check that the input pairs are of the same type | |
137 ## otherwise STARsolo will run for a long time and then error out. | |
138 ## We consume either repeats of two inputs R1 + R2 | |
139 ## or a collection of paired reads. | |
140 #if str($sc.input_types.use) == "repeat": | |
141 #set $reads1 = [] | |
142 #set $reads2 = [] | |
143 #for $r1, $r2 in zip($sc.input_types.input1, $sc.input_types.input2): | |
144 #assert $r1.datatype == $r2.datatype | |
145 #silent $reads1.append(str($r1)) | |
146 #silent $reads2.append(str($r2)) | |
147 #end for | |
148 #set $reads1 = ','.join($reads1) | |
149 #set $reads2 = ','.join($reads2) | |
150 #elif str($sc.input_types.use) == "list_paired": | |
151 #set $r1 = $sc.input_types.input_collection.forward | |
152 #set $r2 = $sc.input_types.input_collection.reverse | |
153 #set $reads1 = $r1 | |
154 #set $reads2 = $r2 | |
155 #end if | |
156 ## cDNA sequence(s) [R2] always go first, then barcode(s) [R1] | |
157 ## see: Section 3.2 of STAR manual for multiple inputs, and Section 13 for STARsolo inputs | |
158 --readFilesIn $reads2 $reads1 | |
159 --soloCBmatchWLtype $sc.soloCBmatchWLtype | |
160 #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'): | |
161 @FASTQ_GZ_OPTION@ | |
162 #end if | |
163 ]]></token> | |
125 <xml name="ref_selection"> | 164 <xml name="ref_selection"> |
126 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> | 165 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> |
127 <!-- Currently, this parameter is not exposed in the wrapper, | 166 <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/> |
128 but used only in the tests to avoid excessive index sizes for | |
129 the tiny test genomes. --> | |
130 <param name="genomeSAindexNbases" type="hidden" value="" /> | |
131 </xml> | 167 </xml> |
132 <xml name="stdio" > | 168 <xml name="stdio" > |
133 <stdio> | 169 <stdio> |
134 <regex match="FATAL error" source="both" level="fatal"/> | 170 <regex match="FATAL error" source="both" level="fatal"/> |
135 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/> | 171 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/> |
136 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> | 172 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> |
137 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> | 173 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> |
138 <yield /> | 174 <yield /> |
139 </stdio> | 175 </stdio> |
140 </xml> | 176 </xml> |
177 <xml name="input_selection"> | |
178 <conditional name="input_types" > | |
179 <param name="use" type="select" label="Input Type" > | |
180 <option value="repeat" >Separate barcode and cDNA reads</option> | |
181 <option value="list_paired" >Paired collection of barcode and cDNA reads</option> | |
182 </param> | |
183 <when value="repeat"> | |
184 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true" | |
185 label="RNA-Seq FASTQ/FASTA file, Barcode reads" /> | |
186 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true" | |
187 label="RNA-Seq FASTQ/FASTA file, cDNA reads"/> | |
188 </when> | |
189 <when value="list_paired"> | |
190 <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs" /> | |
191 </when> | |
192 </conditional> | |
193 </xml> | |
194 <xml name="input_selection_smart_seq"> | |
195 <conditional name="input_types_smart_seq" > | |
196 <param name="use" type="select" label="Input Type" > | |
197 <option value="list_single_end" >Single-end FASTQ collection</option> | |
198 <option value="list_paired_end" >Paired FASTQ collection</option> | |
199 </param> | |
200 <when value="list_single_end"> | |
201 <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files" /> | |
202 </when> | |
203 <when value="list_paired_end"> | |
204 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" /> | |
205 </when> | |
206 </conditional> | |
207 </xml> | |
208 <xml name="umidedup_options"> | |
209 <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other</option> | |
210 <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option> | |
211 <option value="1MM_Directional" >Directional with stringent UMI deduplication</option> | |
212 </xml> | |
213 <xml name="anchor_types"> | |
214 <option value="0">Read start</option> | |
215 <option value="1">Read end</option> | |
216 <option value="2">Adapter start</option> | |
217 <option value="3">Adapter end</option> | |
218 </xml> | |
219 <xml name="cb_match_wl_common"> | |
220 <option value="Exact" >Exact</option> | |
221 <option value="1MM" >Single match</option> | |
222 </xml> | |
223 <xml name="cb_match_wl_cellranger"> | |
224 <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option> | |
225 <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option> | |
226 <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3)</option> | |
227 </xml> | |
228 <xml name="solo_adapter_params"> | |
229 <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." > | |
230 <sanitizer> | |
231 <valid initial="string.digits"> | |
232 <add value="-"/> | |
233 <add value="A"/> | |
234 <add value="T"/> | |
235 <add value="C"/> | |
236 <add value="G"/> | |
237 <add value="N"/> | |
238 </valid> | |
239 </sanitizer> | |
240 </param> | |
241 <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence" /> | |
242 <param argument="--clipAdapterType" type="select" > | |
243 <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option> | |
244 <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option> | |
245 <option value="None" >No adapter clipping</option> | |
246 </param> | |
247 </xml> | |
141 </macros> | 248 </macros> |