comparison macros.xml @ 9:ec9cbd6b9a49 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
author iuc
date Fri, 15 Jan 2021 17:39:11 +0000
parents 00fbfac99d39
children a6fba3d92531
comparison
equal deleted inserted replaced
8:00fbfac99d39 9:ec9cbd6b9a49
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@">2.7.6a</token> 8 <token name="@VERSION@">2.7.7a</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
31 </edam_topics> 31 </edam_topics>
32 <edam_operations> 32 <edam_operations>
33 <edam_operation>operation_0292</edam_operation> 33 <edam_operation>operation_0292</edam_operation>
34 </edam_operations> 34 </edam_operations>
35 </xml> 35 </xml>
36 36
37 <xml name="index_selection" token_with_gene_model="0"> 37 <xml name="index_selection" token_with_gene_model="0">
38 <param argument="--genomeDir" name="genomeDir" type="select" 38 <param argument="--genomeDir" name="genomeDir" type="select"
39 label="Select reference genome" 39 label="Select reference genome"
40 help="If your genome of interest is not listed, contact the Galaxy team"> 40 help="If your genome of interest is not listed, contact the Galaxy team">
41 <options from_data_table="@IDX_DATA_TABLE@"> 41 <options from_data_table="@IDX_DATA_TABLE@">
130 #end if 130 #end if
131 #end if 131 #end if
132 #end if 132 #end if
133 #end if 133 #end if
134 ]]></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>
135 <xml name="ref_selection"> 164 <xml name="ref_selection">
136 <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" />
137 <!-- Currently, this parameter is not exposed in the wrapper, 166 <!-- Currently, this parameter is not exposed in the wrapper,
138 but used only in the tests to avoid excessive index sizes for 167 but used only in the tests to avoid excessive index sizes for
139 the tiny test genomes. --> 168 the tiny test genomes. -->
146 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> 175 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
147 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> 176 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
148 <yield /> 177 <yield />
149 </stdio> 178 </stdio>
150 </xml> 179 </xml>
180 <xml name="input_selection">
181 <conditional name="input_types" >
182 <param name="use" type="select" label="Input Type" >
183 <option value="repeat" >Separate barcode and cDNA reads</option>
184 <option value="list_paired" >Paired collection of barcode and cDNA reads</option>
185 </param>
186 <when value="repeat">
187 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true"
188 label="RNA-Seq FASTQ/FASTA file, Barcode reads" />
189 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true"
190 label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
191 </when>
192 <when value="list_paired">
193 <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs" />
194 </when>
195 </conditional>
196 </xml>
197 <xml name="input_selection_smart_seq">
198 <conditional name="input_types_smart_seq" >
199 <param name="use" type="select" label="Input Type" >
200 <option value="list_single_end" >Single-end FASTQ collection</option>
201 <option value="list_paired_end" >Paired FASTQ collection</option>
202 </param>
203 <when value="list_single_end">
204 <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" />
205 </when>
206 <when value="list_paired_end">
207 <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" />
208 </when>
209 </conditional>
210 </xml>
211 <xml name="umidedup_options">
212 <option value="1MM_All" selected="true">All</option>
213 <option value="1MM_Directional" >Directional</option>
214 </xml>
215 <xml name="anchor_types">
216 <option value="0">Read start</option>
217 <option value="1">Read end</option>
218 <option value="2">Adapter start</option>
219 <option value="3">Adapter end</option>
220 </xml>
221 <xml name="cb_match_wl_common">
222 <option value="Exact" >Exact</option>
223 <option value="1MM" >Single match</option>
224 </xml>
225 <xml name="cb_match_wl_cellranger">
226 <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option>
227 <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option>
228 </xml>
151 </macros> 229 </macros>