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comparison alevin.xml @ 10:e4c01dcece8b draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
author bgruening
date Thu, 22 Jul 2021 14:05:58 +0000
parents ecb9ea6269ee
children e661a3269313
comparison
equal deleted inserted replaced
9:ecb9ea6269ee 10:e4c01dcece8b
1 <tool id="alevin" name="Alevin" version="@VERSION@+galaxy2"> 1 <tool id="alevin" name="Alevin" version="@VERSION@+@GALAXY_VERSION@" profile="@PROFILE_VERSION@">
2 <description>Quantification and analysis of 3’ tagged-end single-cell sequencing data</description> 2 <description>Quantification and analysis of 3’ tagged-end single-cell sequencing data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
44 #end if 44 #end if
45 45
46 && ln -s '${tgmap}' ./alevinmap.tsv 46 && ln -s '${tgmap}' ./alevinmap.tsv
47 && salmon alevin -l 47 && salmon alevin -l
48 #if $pairstraight.readselect == 'paired': 48 #if $pairstraight.readselect == 'paired':
49 ${pairstraight.orientation}${pairstraight.strandedness} 49 #if $pairstraight.libtype.strandedness == 'A'
50 A
51 #else
52 ${pairstraight.libtype.orientation}${pairstraight.libtype.strandedness}
53 #end if
50 -i $index_path 54 -i $index_path
51 -1 ./mate1.fastq 55 -1 ./mate1.fastq
52 -2 ./mate2.fastq 56 -2 ./mate2.fastq
53 #else: 57 #else:
54 '${pairstraight.strandedness}' 58 '${pairstraight.libtype.strandedness}'
55 -i $index_path 59 -i $index_path
56 -r zcat ./unmate.fastq 60 -r zcat ./unmate.fastq
57 #end if 61 #end if
58 -o ./output 62 -o ./output
59 -p "\${GALAXY_SLOTS:-4}" 63 -p "\${GALAXY_SLOTS:-4}"
124 <option value="unmated">Single-end</option> 128 <option value="unmated">Single-end</option>
125 </param> 129 </param>
126 <when value="paired"> 130 <when value="paired">
127 <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="CB+UMI raw sequence file(s)"/> 131 <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="CB+UMI raw sequence file(s)"/>
128 <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="Read-sequence file(s)"/> 132 <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="Read-sequence file(s)"/>
129 <expand macro="orient"/> 133 <expand macro="stranded_pe"/>
130 <expand macro="stranded"/>
131 </when> 134 </when>
132 <when value="unmated"> 135 <when value="unmated">
133 <param name="unmatedreads" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Unmated reads files"/> 136 <param name="unmatedreads" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Unmated reads files"/>
134 <expand macro="stranded"/> 137 <expand macro="stranded_se"/>
135 </when> 138 </when>
136 </conditional> 139 </conditional>
137 <param name="protocol" type="select"> 140 <param name="protocol" type="select">
138 <option value="--dropseq">DropSeq Single Cell protocol</option> 141 <option value="--dropseq">DropSeq Single Cell protocol</option>
139 <option value="--chromium">10x chromium v2 Single Cell protocol</option> 142 <option value="--chromium">10x chromium v2 Single Cell protocol</option>
163 <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/> 166 <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/>
164 <param name="freqThreshold" type="integer" optional="true" help="Minimum frequency for a barcode to be considered. Defaults to 10"/> 167 <param name="freqThreshold" type="integer" optional="true" help="Minimum frequency for a barcode to be considered. Defaults to 10"/>
165 </section> 168 </section>
166 </inputs> 169 </inputs>
167 <outputs> 170 <outputs>
168 <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv"> 171 <data name="quants_mat_tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv">
169 <filter>optional["dumpMtx"] is not True</filter> 172 <filter>optional["dumpMtx"] is not True</filter>
170 </data> 173 </data>
171 <data name="quants_mat.mtx" label="quants_mat.mtx" format="mtx" from_work_dir="output/alevin/quants_mat.mtx"> 174 <data name="quants_mat_mtx" label="quants_mat.mtx" format="mtx" from_work_dir="output/alevin/quants_mat.mtx">
172 <filter>optional["dumpMtx"]</filter> 175 <filter>optional["dumpMtx"]</filter>
173 </data> 176 </data>
174 <data name="raw_cb_frequency.txt" label="raw_cb_frequency.txt" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt"> 177 <data name="raw_cb_frequency_txt" label="raw_cb_frequency.txt" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt">
175 <filter>optional["dumpFeatures"]</filter> 178 <filter>optional["dumpFeatures"]</filter>
176 </data> 179 </data>
177 <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/> 180 <data name="quants_mat_cols_txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
178 <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/> 181 <data name="quants_mat_rows_txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
179 <data name="quants_tier_mat" label="quants_tier_mat" format="mtx" from_work_dir="output/alevin/quants_tier_mat"/> 182 <data name="quants_tier_mat" label="quants_tier_mat" format="mtx" from_work_dir="output/alevin/quants_tier_mat"/>
180 <data name="alevin.log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log"> 183 <data name="alevin_log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">
181 <filter>allout</filter> 184 <filter>allout</filter>
182 </data> 185 </data>
183 <data name="featureDump.txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/> 186 <data name="featureDump_txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
184 <data name="whitelist.txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/> 187 <data name="whitelist_txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
185 <data name="bfh.txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt"> 188 <data name="bfh_txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt">
186 <filter>optional["dumpBfh"]</filter> 189 <filter>optional["dumpBfh"]</filter>
187 </data> 190 </data>
188 <data name="quants_mean_mat" label="quants_mean_mat" format="mtx" from_work_dir="output/alevin/quants_mean_mat"> 191 <data name="quants_mean_mat" label="quants_mean_mat" format="mtx" from_work_dir="output/alevin/quants_mean_mat">
189 <filter>optional["numCellBootstraps"]</filter> 192 <filter>optional["numCellBootstraps"]</filter>
190 </data> 193 </data>
191 <data name="quants_var_mat" label="quants_var_mat" format="mtx" from_work_dir="output/alevin/quants_var_mat"> 194 <data name="quants_var_mat" label="quants_var_mat" format="mtx" from_work_dir="output/alevin/quants_var_mat">
192 <filter>optional["numCellBootstraps"]</filter> 195 <filter>optional["numCellBootstraps"]</filter>
193 </data> 196 </data>
194 <data name="quants_boot_rows.txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt"> 197 <data name="quants_boot_rows_txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
195 <filter>optional["numCellBootstraps"]</filter> 198 <filter>optional["numCellBootstraps"]</filter>
196 </data> 199 </data>
197 <data name="alevinmeta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/alevin_meta_info.json"> 200 <data name="alevinmeta_info_json" format="json" label="meta_info.json" from_work_dir="output/aux_info/alevin_meta_info.json">
198 <filter>allout</filter> 201 <filter>allout</filter>
199 </data> 202 </data>
200 <data name="ambig_info.tsv" format="tsv" label="ambig_info.tsv" from_work_dir="output/aux_info/ambig_info.tsv"> 203 <data name="ambig_info_tsv" format="tsv" label="ambig_info.tsv" from_work_dir="output/aux_info/ambig_info.tsv">
201 <filter>allout</filter> 204 <filter>allout</filter>
202 </data> 205 </data>
203 <data name="meta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json"> 206 <data name="meta_info_json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json">
204 <filter>allout</filter> 207 <filter>allout</filter>
205 </data> 208 </data>
206 <data name="expected_bias" format="txt" label="expected_bias" from_work_dir="output/aux_info/fld"/> 209 <data name="expected_bias" format="txt" label="expected_bias" from_work_dir="output/aux_info/fld"/>
207 <data name="observed_bias" format="txt" label="observed_bias" from_work_dir="output/aux_info/observed_bias"/> 210 <data name="observed_bias" format="txt" label="observed_bias" from_work_dir="output/aux_info/observed_bias"/>
208 <data name="observed_bias_3p" format="txt" label="observed_bias_3p" from_work_dir="output/aux_info/observed_bias_3p"/> 211 <data name="observed_bias_3p" format="txt" label="observed_bias_3p" from_work_dir="output/aux_info/observed_bias_3p"/>
209 <data name="flenDist.txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/> 212 <data name="flenDist_txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/>
210 <data name="salmon_quant.log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log"> 213 <data name="salmon_quant_log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">
211 <filter>allout</filter> 214 <filter>allout</filter>
212 </data> 215 </data>
213 <collection name="umigraphs" type="list" label="Umi graph PDFs"> 216 <collection name="umigraphs" type="list" label="Umi graph PDFs">
214 <filter>optional["dumpUmiGraph"]</filter> 217 <filter>optional["dumpUmiGraph"]</filter>
215 <discover_datasets pattern="__name_and_ext__" ext="pdf" directory="fixed"/> 218 <discover_datasets pattern="__name_and_ext__" ext="pdf" directory="fixed"/>
239 <param name="keepCBFraction" value="1"/> 242 <param name="keepCBFraction" value="1"/>
240 <param name="dumpFeatures" value="Yes"/> 243 <param name="dumpFeatures" value="Yes"/>
241 <param name="freqThreshold" value="5"/> 244 <param name="freqThreshold" value="5"/>
242 <param name="dumpMtx" value="Yes"/> 245 <param name="dumpMtx" value="Yes"/>
243 </section> 246 </section>
244 <output name="quants_mat.mtx" file="alevin_mat.mtx" ftype="mtx"/> 247 <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true" lines_diff="62"/>
245 </test> 248 </test>
246 <test expect_num_outputs="14"> 249 <test expect_num_outputs="14">
247 <conditional name="refTranscriptSource"> 250 <conditional name="refTranscriptSource">
248 <param name="TranscriptSource" value="history"/> 251 <param name="TranscriptSource" value="history"/>
249 <section name="s_index"> 252 <section name="s_index">
264 <param name="dumpFeatures" value="Yes"/> 267 <param name="dumpFeatures" value="Yes"/>
265 <param name="numCellBootstraps" value="2"/> 268 <param name="numCellBootstraps" value="2"/>
266 <param name="freqThreshold" value="5"/> 269 <param name="freqThreshold" value="5"/>
267 <param name="dumpMtx" value="Yes"/> 270 <param name="dumpMtx" value="Yes"/>
268 </section> 271 </section>
269 <output name="quants_mat.mtx" file="alevin_mat.mtx" ftype="mtx"/> 272 <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true" lines_diff="62"/>
270 </test> 273 </test>
271 </tests> 274 </tests>
272 <help><![CDATA[ 275 <help><![CDATA[
273 @salmonhelp@ 276 @salmonhelp@
274 @alevinhelp@ 277 @alevinhelp@