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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit f523cd10a711b70ae4fef91a6e4dbc02781858b9
author iuc
date Mon, 15 May 2023 10:03:25 +0000
parents 81ad264c1548
children
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0:81ad264c1548 1:4a75f9c84a4b
1 <tool id="velocyto_cli" name="velocyto CLI" version="@VERSION@+galaxy0"> 1 <tool id="velocyto_cli" name="velocyto CLI" version="@VERSION@+galaxy1">
2 <description>pre-process data for the analysis of RNA velocity</description> 2 <description>pre-process data for the analysis of RNA velocity</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edam"/> 6 <expand macro="edam"/>
20 <command> 20 <command>
21 <![CDATA[ 21 <![CDATA[
22 #import re 22 #import re
23 23
24 #if str($main.do) == "run10x": 24 #if str($main.do) == "run10x":
25 #if str($main.sample_definition.sample_definition_select) == "manual":
26 #set sample = str($main.sample_definition.sample)
27 #else:
28 #set sample = re.sub('[^\w\-\s]', '_', str($main.BAM.element_identifier))
29 #end if
25 ## We need to reproduce cell ranger structure: 30 ## We need to reproduce cell ranger structure:
26 mkdir -p '$main.sample/outs/filtered_gene_bc_matrices/whatever/' && 31 mkdir -p '$sample/outs/filtered_gene_bc_matrices/whatever/' &&
27 ln -s '${main.BAM}' '$main.sample/outs/possorted_genome_bam.bam' && 32 ln -s '${main.BAM}' '$sample/outs/possorted_genome_bam.bam' &&
28 ln -s '${main.barcodes}' '$main.sample/outs/filtered_gene_bc_matrices/whatever/barcodes.tsv' && 33 ln -s '${main.barcodes}' '$sample/outs/filtered_gene_bc_matrices/whatever/barcodes.tsv' &&
29 #else if str($main.do) in ['run', 'run-smartseq2']: 34 #else if str($main.do) in ['run', 'run-smartseq2']:
30 #for $bam in $main.bamfiles: 35 #for $bam in $main.bamfiles:
31 #set input_name = re.sub('[^\w\-\s]', '_', str($bam.element_identifier)) 36 #set input_name = re.sub('[^\w\-\s]', '_', str($bam.element_identifier))
32 cp '$bam' '${input_name}.bam' && 37 cp '$bam' '${input_name}.bam' &&
33 #end for 38 #end for
65 #end if 70 #end if
66 $main.M 71 $main.M
67 -t '$main.t' 72 -t '$main.t'
68 @SAMTOOLS_OPTS@ 73 @SAMTOOLS_OPTS@
69 '$verbosity' 74 '$verbosity'
70 '$main.sample' 75 '$sample'
71 '$main.gtffile' 76 '$main.gtffile'
72 && mv '$main.sample/velocyto/'*.loom 'output.loom' 77 && mv '$sample/velocyto/'*.loom 'output.loom'
73 78
74 #else if str($main.do) == "run-smartseq2": 79 #else if str($main.do) == "run-smartseq2":
75 run-smartseq2 80 run-smartseq2
76 @LOOMOUT@ 81 @LOOMOUT@
77 #if str($main.m) != 'None': 82 #if str($main.m) != 'None':
117 <!-- the above are wrappers for the main "run" command --> 122 <!-- the above are wrappers for the main "run" command -->
118 <option value="run" >Analysis for other protocols</option> 123 <option value="run" >Analysis for other protocols</option>
119 <option value="dropest-bc-correct">Correct DropEst barcodes and produce valid barcodes file</option> 124 <option value="dropest-bc-correct">Correct DropEst barcodes and produce valid barcodes file</option>
120 </param> 125 </param>
121 <when value="run10x" > 126 <when value="run10x" >
122 <param name="sample" type="text" value="sample" label="sample name" help="This name will appear as prefix of each cell barcode."> 127 <conditional name="sample_definition">
123 <sanitizer invalid_char=""> 128 <param name="sample_definition_select" type="select" label="How to set sample name" help="This name will appear as prefix of each cell barcode.">
124 <valid initial="string.letters,string.digits"> 129 <option value="manual">Manually</option>
125 <add value="_" /> 130 <option value="identifier">Automatic (use identifier in history)</option>
126 </valid> 131 </param>
127 </sanitizer> 132 <when value="manual">
128 <validator type="regex">[0-9a-zA-Z_]+</validator> 133 <param name="sample" type="text" value="sample" label="sample name" help="">
129 </param> 134 <sanitizer invalid_char="">
135 <valid initial="string.letters,string.digits">
136 <add value="_" />
137 </valid>
138 </sanitizer>
139 <validator type="regex">[0-9a-zA-Z_]+</validator>
140 </param>
141 </when>
142 <when value="identifier"/>
143 </conditional>
130 <param name="BAM" type="data" format="bam" label="BAM file including CB tag" help="Can be Cell ranger output or STAR solo output" /> 144 <param name="BAM" type="data" format="bam" label="BAM file including CB tag" help="Can be Cell ranger output or STAR solo output" />
131 <param name="barcodes" type="data" format="tsv,tabular,txt" label="List of valid cell barcodes" help="Can be STAR solo barcodes output" /> 145 <param name="barcodes" type="data" format="tsv,tabular,txt" label="List of valid cell barcodes" help="Can be STAR solo barcodes output" />
132 <param name="gtffile" type="data" format="gtf" label="GTF file" /> 146 <param name="gtffile" type="data" format="gtf" label="GTF file" />
133 <param argument="-s" type="data" format="csv" optional="true" 147 <param argument="-s" type="data" format="csv" optional="true"
134 label="Metadata Table" 148 label="Metadata Table"
190 <tests> 204 <tests>
191 <!-- Test 1 10x --> 205 <!-- Test 1 10x -->
192 <test expect_num_outputs="1"> 206 <test expect_num_outputs="1">
193 <conditional name="main"> 207 <conditional name="main">
194 <param name="do" value="run10x"/> 208 <param name="do" value="run10x"/>
195 <param name="sample" value="sample"/> 209 <conditional name="sample_definition">
210 <param name="sample_definition_select" value="manual"/>
211 <param name="sample" value="sample"/>
212 </conditional>
196 <param name="BAM" value="STARsolo_allSAMat.bam"/> 213 <param name="BAM" value="STARsolo_allSAMat.bam"/>
197 <param name="barcodes" value="barcodes.tsv"/> 214 <param name="barcodes" value="barcodes.tsv"/>
198 <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/> 215 <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
199 <param name="M" value="false"/> 216 <param name="M" value="false"/>
200 <param name="t" value="uint16"/> 217 <param name="t" value="uint16"/>
207 <metadata name="layers_count" value="3" /> 224 <metadata name="layers_count" value="3" />
208 <metadata name="layers_names" value="ambiguous,spliced,unspliced" /> 225 <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
209 <metadata name="col_attrs_count" value="1" /> 226 <metadata name="col_attrs_count" value="1" />
210 <metadata name="col_attrs_names" value="CellID" /> 227 <metadata name="col_attrs_names" value="CellID" />
211 </output> 228 </output>
229 <assert_command>
230 <has_text text="sample"/>
231 </assert_command>
212 <assert_stdout> 232 <assert_stdout>
213 <has_text text="Counting for batch 1, containing 6 cells and 10 reads"/> 233 <has_text text="Counting for batch 1, containing 6 cells and 10 reads"/>
214 </assert_stdout> 234 </assert_stdout>
215 </test> 235 </test>
216 <!-- Test 2 run single bam as single cell --> 236 <!-- Test 2 run single bam as single cell -->
217 <test expect_num_outputs="1"> 237 <test expect_num_outputs="1">
218 <conditional name="main"> 238 <conditional name="main">
260 <metadata name="col_attrs_names" value="CellID" /> 280 <metadata name="col_attrs_names" value="CellID" />
261 </output> 281 </output>
262 <assert_stdout> 282 <assert_stdout>
263 <has_text text="Counting for batch 2, containing 1 cells and 716 reads"/> 283 <has_text text="Counting for batch 2, containing 1 cells and 716 reads"/>
264 </assert_stdout> 284 </assert_stdout>
265 </test> 285 </test>
286 <!-- Test 4 10x indentifyer -->
287 <test expect_num_outputs="1">
288 <conditional name="main">
289 <param name="do" value="run10x"/>
290 <conditional name="sample_definition">
291 <param name="sample_definition_select" value="identifier"/>
292 </conditional>
293 <param name="BAM" value="STARsolo_allSAMat.bam"/>
294 <param name="barcodes" value="barcodes.tsv"/>
295 <param name="gtffile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf"/>
296 <param name="M" value="false"/>
297 <param name="t" value="uint16"/>
298 </conditional>
299 <output name="samples">
300 <assert_contents>
301 <has_size value="25996" delta="3000"/>
302 </assert_contents>
303 <metadata name="row_attrs_count" value="6" />
304 <metadata name="layers_count" value="3" />
305 <metadata name="layers_names" value="ambiguous,spliced,unspliced" />
306 <metadata name="col_attrs_count" value="1" />
307 <metadata name="col_attrs_names" value="CellID" />
308 </output>
309 <assert_command>
310 <has_text text="STARsolo_allSAMat"/>
311 <not_has_text text="sample"/>
312 </assert_command>
313 <assert_stdout>
314 <has_text text="Counting for batch 1, containing 6 cells and 10 reads"/>
315 </assert_stdout>
316 </test>
266 </tests> 317 </tests>
267 <help><![CDATA[ 318 <help><![CDATA[
268 Requirements on the input files 319 Requirements on the input files
269 320
270 velocyto assumes that the bam file that is passed to the CLI contains a set of information and that some upstream analysis was performed on them already. In particular the bam file will have to: 321 velocyto assumes that the bam file that is passed to the CLI contains a set of information and that some upstream analysis was performed on them already. In particular the bam file will have to: