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comparison data_manager/macros.xml @ 10:f639ff7dea45 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 1f8b01701c5b81d155617267a179ba42a0d4a307"
author iuc
date Fri, 10 Sep 2021 16:42:21 +0000
parents 5750f6d0d369
children c6f957c373d3
comparison
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9:5750f6d0d369 10:f639ff7dea45
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>