Mercurial > repos > bgruening > alevin
comparison alevin.xml @ 4:917f8e439160 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
author | bgruening |
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date | Wed, 06 Nov 2019 13:54:21 -0500 |
parents | 0a5258e41227 |
children | ff78e9c7b0d8 |
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3:0a5258e41227 | 4:917f8e439160 |
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1 <tool id="alevin" name="Alevin" version="@VERSION@"> | 1 <tool id="alevin" name="Alevin" version="@VERSION@+galaxy1"> |
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"/> |
88 #if $optional.lowRegionMinNumBarcodes: | 88 #if $optional.lowRegionMinNumBarcodes: |
89 --lowregionMinNumBarcodes '${optional.lowRegionMinNumBarcodes}' | 89 --lowregionMinNumBarcodes '${optional.lowRegionMinNumBarcodes}' |
90 #end if | 90 #end if |
91 #if $optional.maxNumBarcodes: | 91 #if $optional.maxNumBarcodes: |
92 --maxNumBarcodes '${optional.maxNumBarcodes}' | 92 --maxNumBarcodes '${optional.maxNumBarcodes}' |
93 #end if | |
94 #if $optional.freqThreshold: | |
95 --freqThreshold '${optional.freqThreshold}' | |
93 #end if | 96 #end if |
94 | 97 |
95 #if $optional.dumpMtx != "--dumpMtx": | 98 #if $optional.dumpMtx != "--dumpMtx": |
96 && python '$__tool_directory__/vpolo_convert.py' -m | 99 && python '$__tool_directory__/vpolo_convert.py' -m |
97 #end if | 100 #end if |
143 <param name="numCellBootstraps" type="integer" optional="true" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/> | 146 <param name="numCellBootstraps" type="integer" optional="true" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/> |
144 <param name="minScoreFraction" type="float" optional="true" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads). The argument to --minScoreFraction determines what fraction of the maximum score s a mapping must achieve to be potentially retained. For a minimum score fraction of f, only mappings with a score less than (f * s) will be kept. Mappings with lower scores will be considered as low-quality, and will be discarded."/> | 147 <param name="minScoreFraction" type="float" optional="true" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads). The argument to --minScoreFraction determines what fraction of the maximum score s a mapping must achieve to be potentially retained. For a minimum score fraction of f, only mappings with a score less than (f * s) will be kept. Mappings with lower scores will be considered as low-quality, and will be discarded."/> |
145 <param name="keepCBFraction" type="float" optional="true" help="Fraction of cellular barcodes to keep (Between 0 and 1)."/> | 148 <param name="keepCBFraction" type="float" optional="true" help="Fraction of cellular barcodes to keep (Between 0 and 1)."/> |
146 <param name="lowRegionMinNumBarcodes" type="integer" optional="true" help="Minimum number of cell barcodes to use fo learning low confidence region (defaults to 200)"/> | 149 <param name="lowRegionMinNumBarcodes" type="integer" optional="true" help="Minimum number of cell barcodes to use fo learning low confidence region (defaults to 200)"/> |
147 <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/> | 150 <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/> |
151 <param name="freqThreshold" type="integer" optional="true" help="Minimum frequency for a barcode to be considered. Defaults to 10"/> | |
148 </section> | 152 </section> |
149 </inputs> | 153 </inputs> |
150 <outputs> | 154 <outputs> |
151 <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv"> | 155 <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv"> |
152 <filter>optional["dumpMtx"] is not True</filter> | 156 <filter>optional["dumpMtx"] is not True</filter> |
153 </data> | 157 </data> |
154 <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz"> | 158 <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz"> |
155 <filter>optional["dumpMtx"]</filter> | 159 <filter>optional["dumpMtx"]</filter> |
160 </data> | |
161 <data name="raw_cb_frequency.txt" label="raw_cb_frequency.txt" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt"> | |
162 <filter>optional["dumpFeatures"]</filter> | |
156 </data> | 163 </data> |
157 <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/> | 164 <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/> |
158 <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/> | 165 <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/> |
159 <data name="quants_tier_mat.gz" label="quants_tier_mat.gz" format="mtx" from_work_dir="output/alevin/quants_tier_mat.gz"/> | 166 <data name="quants_tier_mat.gz" label="quants_tier_mat.gz" format="mtx" from_work_dir="output/alevin/quants_tier_mat.gz"/> |
160 <data name="alevin.log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log"> | 167 <data name="alevin.log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log"> |
194 <filter>optional["dumpUmiGraph"]</filter> | 201 <filter>optional["dumpUmiGraph"]</filter> |
195 <discover_datasets pattern="__name_and_ext__" ext="pdf" directory="fixed"/> | 202 <discover_datasets pattern="__name_and_ext__" ext="pdf" directory="fixed"/> |
196 </collection> | 203 </collection> |
197 </outputs> | 204 </outputs> |
198 <tests> | 205 <tests> |
199 <test expect_num_outputs="10"> | 206 <test expect_num_outputs="11"> |
200 <conditional name="refTranscriptSource"> | 207 <conditional name="refTranscriptSource"> |
201 <param name="TranscriptSource" value="history"/> | 208 <param name="TranscriptSource" value="history"/> |
202 <section name="s_index"> | 209 <section name="s_index"> |
203 <param name="fasta" value="minitranscript.fa"/> | 210 <param name="fasta" value="minitranscript.fa"/> |
204 </section> | 211 </section> |
211 <param name="strandedness" value="SR"/> | 218 <param name="strandedness" value="SR"/> |
212 </conditional> | 219 </conditional> |
213 <param name="protocol" value="--chromium"/> | 220 <param name="protocol" value="--chromium"/> |
214 <param name="tgmap" value="minitxp.tsv"/> | 221 <param name="tgmap" value="minitxp.tsv"/> |
215 <param name="dumpMtx" value="Yes"/> | 222 <param name="dumpMtx" value="Yes"/> |
223 <param name="freqThreshold" value="5"/> | |
224 <param name="dumpFeatures" value="Yes"/> | |
225 <param name="keepCBFraction" value="1"/> | |
216 <output name="quants_mat.mtx.gz" file="alevin_mat.mtx.gz" ftype="mtx" compare="sim_size"/> | 226 <output name="quants_mat.mtx.gz" file="alevin_mat.mtx.gz" ftype="mtx" compare="sim_size"/> |
217 </test> | 227 </test> |
218 </tests> | 228 </tests> |
219 <help><![CDATA[ | 229 <help><![CDATA[ |
220 @salmonhelp@ | 230 @salmonhelp@ |