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comparison alevin.xml @ 7:ff78e9c7b0d8 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
author bgruening
date Sat, 03 Oct 2020 18:21:49 +0000
parents 917f8e439160
children 04b494623f8e
comparison
equal deleted inserted replaced
6:53d74155bb52 7:ff78e9c7b0d8
1 <tool id="alevin" name="Alevin" version="@VERSION@+galaxy1"> 1 <tool id="alevin" name="Alevin" version="@VERSION@+galaxy2">
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"/>
95 --freqThreshold '${optional.freqThreshold}' 95 --freqThreshold '${optional.freqThreshold}'
96 #end if 96 #end if
97 97
98 #if $optional.dumpMtx != "--dumpMtx": 98 #if $optional.dumpMtx != "--dumpMtx":
99 && python '$__tool_directory__/vpolo_convert.py' -m 99 && python '$__tool_directory__/vpolo_convert.py' -m
100 #else:
101 && gunzip output/alevin/quants_mat.mtx.gz
100 #end if 102 #end if
101 #if $optional.dumpUmiGraph: 103 #if $optional.dumpUmiGraph:
102 && python '$__tool_directory__/vpolo_convert.py' -u 104 && python '$__tool_directory__/vpolo_convert.py' -u
103 && sh '$__tool_directory__/umiout.sh' 105 && sh '$__tool_directory__/umiout.sh'
104 #end if 106 #end if
107
108 && gunzip output/alevin/quants_tier_mat.gz
109 #if $optional.numCellBootstraps:
110 && gunzip output/alevin/quants_mean_mat.gz
111 && gunzip output/alevin/quants_var_mat.gz
112 #end if
113
114 && gunzip output/aux_info/fld.gz
115 && gunzip output/aux_info/observed_bias.gz
116 && gunzip output/aux_info/observed_bias_3p.gz
105 ]]> 117 ]]>
106 </command> 118 </command>
107 <inputs> 119 <inputs>
108 <expand macro="index"/> 120 <expand macro="index"/>
109 <conditional name="pairstraight"> 121 <conditional name="pairstraight">
142 <param name="dumpUmiGraph" type="boolean" truevalue="--dumpUmiGraph" falsevalue="" checked="false" help="Dump the per-cell level umi graph"/> 154 <param name="dumpUmiGraph" type="boolean" truevalue="--dumpUmiGraph" falsevalue="" checked="false" help="Dump the per-cell level umi graph"/>
143 <param name="dumpMtx" type="boolean" truevalue="--dumpMtx" falsevalue="" checked="false" help="Converts the default binary format of alevin for gene-count matrix into a human readable mtx (matrix market exchange) sparse format."/> 155 <param name="dumpMtx" type="boolean" truevalue="--dumpMtx" falsevalue="" checked="false" help="Converts the default binary format of alevin for gene-count matrix into a human readable mtx (matrix market exchange) sparse format."/>
144 <param name="forceCells" type="integer" optional="true" help="Explicitly specify the number of cells."/> 156 <param name="forceCells" type="integer" optional="true" help="Explicitly specify the number of cells."/>
145 <param name="expectCells" type="integer" optional="true" help="define a close upper bound on expected number of cells."/> 157 <param name="expectCells" type="integer" optional="true" help="define a close upper bound on expected number of cells."/>
146 <param name="numCellBootstraps" type="integer" optional="true" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/> 158 <param name="numCellBootstraps" type="integer" optional="true" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/>
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."/> 159 <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).
160 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."/>
148 <param name="keepCBFraction" type="float" optional="true" help="Fraction of cellular barcodes to keep (Between 0 and 1)."/> 161 <param name="keepCBFraction" type="float" optional="true" help="Fraction of cellular barcodes to keep (Between 0 and 1)."/>
149 <param name="lowRegionMinNumBarcodes" type="integer" optional="true" help="Minimum number of cell barcodes to use fo learning low confidence region (defaults to 200)"/> 162 <param name="lowRegionMinNumBarcodes" type="integer" optional="true" help="Minimum number of cell barcodes to use fo learning low confidence region (defaults to 200)"/>
150 <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/> 163 <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"/> 164 <param name="freqThreshold" type="integer" optional="true" help="Minimum frequency for a barcode to be considered. Defaults to 10"/>
152 </section> 165 </section>
153 </inputs> 166 </inputs>
154 <outputs> 167 <outputs>
155 <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv"> 168 <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv">
156 <filter>optional["dumpMtx"] is not True</filter> 169 <filter>optional["dumpMtx"] is not True</filter>
157 </data> 170 </data>
158 <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz"> 171 <data name="quants_mat.mtx" label="quants_mat.mtx" format="mtx" from_work_dir="output/alevin/quants_mat.mtx">
159 <filter>optional["dumpMtx"]</filter> 172 <filter>optional["dumpMtx"]</filter>
160 </data> 173 </data>
161 <data name="raw_cb_frequency.txt" label="raw_cb_frequency.txt" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt"> 174 <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> 175 <filter>optional["dumpFeatures"]</filter>
163 </data> 176 </data>
164 <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/> 177 <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
165 <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/> 178 <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
166 <data name="quants_tier_mat.gz" label="quants_tier_mat.gz" format="mtx" from_work_dir="output/alevin/quants_tier_mat.gz"/> 179 <data name="quants_tier_mat" label="quants_tier_mat" format="mtx" from_work_dir="output/alevin/quants_tier_mat"/>
167 <data name="alevin.log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log"> 180 <data name="alevin.log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">
168 <filter>allout</filter> 181 <filter>allout</filter>
169 </data> 182 </data>
170 <data name="featureDump.txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/> 183 <data name="featureDump.txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
171 <data name="whitelist.txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/> 184 <data name="whitelist.txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
172 <data name="bfh.txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt"> 185 <data name="bfh.txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt">
173 <filter>optional["dumpBfh"]</filter> 186 <filter>optional["dumpBfh"]</filter>
174 </data> 187 </data>
175 <data name="quants_mean_mat.gz" label="quants_mean_mat.gz" format="mtx" from_work_dir="output/alevin/quants_mean_mat.gz"> 188 <data name="quants_mean_mat" label="quants_mean_mat" format="mtx" from_work_dir="output/alevin/quants_mean_mat">
176 <filter>optional["numCellBootstraps"]</filter> 189 <filter>optional["numCellBootstraps"]</filter>
177 </data> 190 </data>
178 <data name="quants_var_mat.gz" label="quants_var_mat.gz" format="mtx" from_work_dir="output/alevin/quants_var_mat.gz"> 191 <data name="quants_var_mat" label="quants_var_mat" format="mtx" from_work_dir="output/alevin/quants_var_mat">
179 <filter>optional["numCellBootstraps"]</filter> 192 <filter>optional["numCellBootstraps"]</filter>
180 </data> 193 </data>
181 <data name="quants_boot_rows.txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt"> 194 <data name="quants_boot_rows.txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
182 <filter>optional["numCellBootstraps"]</filter> 195 <filter>optional["numCellBootstraps"]</filter>
183 </data> 196 </data>
188 <filter>allout</filter> 201 <filter>allout</filter>
189 </data> 202 </data>
190 <data name="meta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json"> 203 <data name="meta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json">
191 <filter>allout</filter> 204 <filter>allout</filter>
192 </data> 205 </data>
193 <data name="expected_bias.gz" format="txt" label="expected_bias.gz" from_work_dir="output/aux_info/fld.gz"/> 206 <data name="expected_bias" format="txt" label="expected_bias" from_work_dir="output/aux_info/fld"/>
194 <data name="observed_bias.gz" format="txt" label="observed_bias.gz" from_work_dir="output/aux_info/observed_bias.gz"/> 207 <data name="observed_bias" format="txt" label="observed_bias" from_work_dir="output/aux_info/observed_bias"/>
195 <data name="observed_bias_3p.gz" format="txt" label="observed_bias_3p.gz" from_work_dir="output/aux_info/observed_bias_3p.gz"/> 208 <data name="observed_bias_3p" format="txt" label="observed_bias_3p" from_work_dir="output/aux_info/observed_bias_3p"/>
196 <data name="flenDist.txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/> 209 <data name="flenDist.txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/>
197 <data name="salmon_quant.log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log"> 210 <data name="salmon_quant.log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">
198 <filter>allout</filter> 211 <filter>allout</filter>
199 </data> 212 </data>
200 <collection name="umigraphs" type="list" label="Umi graph PDFs"> 213 <collection name="umigraphs" type="list" label="Umi graph PDFs">
221 <param name="tgmap" value="minitxp.tsv"/> 234 <param name="tgmap" value="minitxp.tsv"/>
222 <param name="dumpMtx" value="Yes"/> 235 <param name="dumpMtx" value="Yes"/>
223 <param name="freqThreshold" value="5"/> 236 <param name="freqThreshold" value="5"/>
224 <param name="dumpFeatures" value="Yes"/> 237 <param name="dumpFeatures" value="Yes"/>
225 <param name="keepCBFraction" value="1"/> 238 <param name="keepCBFraction" value="1"/>
226 <output name="quants_mat.mtx.gz" file="alevin_mat.mtx.gz" ftype="mtx" compare="sim_size"/> 239 <output name="quants_mat.mtx" file="alevin_mat.mtx" ftype="mtx"/>
240 </test>
241 <test expect_num_outputs="14">
242 <conditional name="refTranscriptSource">
243 <param name="TranscriptSource" value="history"/>
244 <section name="s_index">
245 <param name="fasta" value="minitranscript.fa"/>
246 </section>
247 </conditional>
248 <conditional name="pairstraight">
249 <param name="readselect" value="paired"/>
250 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
251 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
252 <param name="orientation" value="I"/>
253 <param name="strandedness" value="SR"/>
254 </conditional>
255 <param name="protocol" value="--chromium"/>
256 <param name="tgmap" value="minitxp.tsv"/>
257 <param name="dumpMtx" value="Yes"/>
258 <param name="freqThreshold" value="5"/>
259 <param name="dumpFeatures" value="Yes"/>
260 <param name="keepCBFraction" value="1"/>
261 <section name="optional">
262 <param name="numCellBootstraps" value="2"/>
263 </section>
264 <output name="quants_mat.mtx" file="alevin_mat.mtx" ftype="mtx"/>
227 </test> 265 </test>
228 </tests> 266 </tests>
229 <help><![CDATA[ 267 <help><![CDATA[
230 @salmonhelp@ 268 @salmonhelp@
231 @alevinhelp@ 269 @alevinhelp@