Mercurial > repos > iuc > purge_dups
comparison purge_dups.xml @ 3:76d4cbefff85 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
author | iuc |
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date | Mon, 14 Jun 2021 18:01:05 +0000 |
parents | 17b378303f2d |
children | a315c25dc813 |
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2:17b378303f2d | 3:76d4cbefff85 |
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1 <tool id="purge_dups" name="Purge overlaps" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> | 1 <tool id="purge_dups" name="Purge overlaps" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> |
2 <description>and haplotigs in an assembly based on read depth (purge_dups)</description> | 2 <description>and haplotigs in an assembly based on read depth (purge_dups)</description> |
3 <macros> | 3 <macros> |
4 <token name="@TOOL_VERSION@">1.2.5</token> | 4 <token name="@TOOL_VERSION@">1.2.5</token> |
5 <token name="@VERSION_SUFFIX@">2</token> | 5 <token name="@VERSION_SUFFIX@">3</token> |
6 <xml name="trimmers"> | |
7 <section name="section_hist" title="Histogram plot options" > | |
8 <!--<param name="cutoffs_his" type="data" optional="true" format="txt" label="Read depth cutoffs file" />--> | |
9 <param argument="--ymin" type="integer" optional="true" min="0" label="Specify a minimum for the Y axis"/> | |
10 <param argument="--ymax" type="integer" optional="true" label="Specify a maximum for the Y axis"/> | |
11 <param argument="--xmin" type="integer" optional="true" min="0" label="Specify a minimum for the X axis"/> | |
12 <param argument="--xmax" type="integer" optional="true" label="Specify a maximum for the X axis"/> | |
13 <param argument="--title" type="text" value="Read depth histogram plot" label="Histogram title"/> | |
14 </section> | |
15 </xml> | |
16 <token name="@HIST_PLOT@"><![CDATA[ | |
17 python '$__tool_directory__/hist_plot.py' | |
18 --cutoffs cutoffs.tsv | |
19 #if $function_select.section_hist.ymin | |
20 --ymin $function_select.section_hist.ymin | |
21 #end if | |
22 #if $function_select.section_hist.ymax | |
23 --ymax $function_select.section_hist.ymax | |
24 #end if | |
25 #if $function_select.section_hist.xmin | |
26 --xmin $function_select.section_hist.xmin | |
27 #end if | |
28 #if $function_select.section_hist.xmax | |
29 --xmax $function_select.section_hist.xmax | |
30 #end if | |
31 #if $function_select.section_hist.title | |
32 --title '${function_select.section_hist.title}' | |
33 #end if | |
34 depth.stat hist.png | |
35 ]]></token> | |
36 <token name="@CALCUTS@"><![CDATA[ | |
37 calcuts | |
38 #if $function_select.section_calcuts.min_depth: | |
39 -f $function_select.section_calcuts.min_depth | |
40 #end if | |
41 #if $function_select.section_calcuts.low_depth: | |
42 -l $function_select.section_calcuts.low_depth | |
43 #end if | |
44 #if $function_select.section_calcuts.transition: | |
45 -m $function_select.section_calcuts.transition | |
46 #end if | |
47 #if $function_select.section_calcuts.upper_depth: | |
48 -u $function_select.section_calcuts.upper_depth | |
49 #end if | |
50 $function_select.section_calcuts.ploidy | |
51 ]]></token> | |
52 <xml name="calcuts"> | |
53 <section name="section_calcuts" title="Calcuts options"> | |
54 <param name="min_depth" type="float" label="Minimum depth count fraction to maximum depth coun" min="0" max="1" argument="-f" optional="true" help="Default = 0.1"/> | |
55 <param name="low_depth" label="Lower bound for read depth" type="integer" argument="-l" optional="true"/> | |
56 <param name="transition" label="Transition between haploid and diploid" type="integer" argument="-m" optional="true"/> | |
57 <param name="upper_depth" label="Upper bound for read depth" type="integer" argument="-u" optional="true"/> | |
58 <param name="ploidy" argument="-d" type="select" label="Ploidy"> | |
59 <option value="-d 0" selected="true">Diploid [0]</option> | |
60 <option value="-d 1">Haploid [1]</option> | |
61 </param> | |
62 </section> | |
63 </xml> | |
6 </macros> | 64 </macros> |
7 <requirements> | 65 <requirements> |
8 <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement> | 66 <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement> |
67 <requirement type="package" version="3.4.2">matplotlib-base</requirement> | |
9 </requirements> | 68 </requirements> |
10 <command detect_errors="exit_code"><![CDATA[ | 69 <command detect_errors="exit_code"><![CDATA[ |
11 #if $function_select.functions == "purge_dups": | 70 #if $function_select.functions == 'purge_dups': |
12 #for $i, $file in enumerate($function_select.input): | 71 #for $i, $file in enumerate($function_select.input): |
13 #if $file.is_of_type("paf"): | 72 #if $file.is_of_type("paf"): |
14 gzip -c '${file}' > '${i}.gz' && | 73 gzip -c '${file}' > '${i}.gz' && |
15 #else | 74 #else |
16 ln -s '${file}' '${i}.gz' && | 75 ln -s '${file}' '${i}.gz' && |
17 #end if | 76 #end if |
18 #end for | 77 #end for |
19 purge_dups | 78 purge_dups |
20 #if $function_select.coverage: | 79 #if $function_select.coverage: |
21 -c '$function_select.coverage' | 80 -c '${function_select.coverage}' |
22 #end if | 81 #end if |
23 #if $function_select.cutoffs: | 82 #if $function_select.cutoffs: |
24 -T '$function_select.cutoffs' | 83 -T '${function_select.cutoffs}' |
25 #end if | 84 #end if |
26 #if $function_select.min_bad: | 85 #if $function_select.min_bad: |
27 -f $function_select.min_bad | 86 -f $function_select.min_bad |
28 #end if | 87 #end if |
29 #if $function_select.min_align: | 88 #if $function_select.min_align: |
36 -m $function_select.min_chain | 95 -m $function_select.min_chain |
37 #end if | 96 #end if |
38 #if $function_select.max_gap: | 97 #if $function_select.max_gap: |
39 -M $function_select.max_gap | 98 -M $function_select.max_gap |
40 #end if | 99 #end if |
41 #if $function_select.double_chain.chaining_rounds == "two": | 100 #if $function_select.double_chain.chaining_rounds == 'two': |
42 -2 | 101 -2 |
43 #if $function_select.double_chain.max_gap_2: | 102 #if $function_select.double_chain.max_gap_2: |
44 -G $function_select.double_chain.max_gap_2 | 103 -G $function_select.double_chain.max_gap_2 |
45 #end if | 104 #end if |
46 #end if | 105 #end if |
52 #end if | 111 #end if |
53 #for $i, $file in enumerate($function_select.input): | 112 #for $i, $file in enumerate($function_select.input): |
54 '${i}.gz' | 113 '${i}.gz' |
55 #end for | 114 #end for |
56 > dups.bed 2> purge_dups.log | 115 > dups.bed 2> purge_dups.log |
57 #else if $function_select.functions == "split_fa": | 116 #else if $function_select.functions == 'split_fa': |
58 split_fa | 117 split_fa |
59 #if $function_select.split: | 118 #if $function_select.split: |
60 -n $function_select.split | 119 -n $function_select.split |
61 #end if | 120 #end if |
62 '$function_select.input' > split.fasta | 121 '${function_select.input}' > split.fasta |
63 #else if $function_select.functions == "pbcstat": | 122 #else if $function_select.functions == 'pbcstat': |
64 #for $i, $file in enumerate($function_select.input): | 123 #for $i, $file in enumerate($function_select.input): |
65 #if $file.is_of_type("paf"): | 124 #if $file.is_of_type('paf'): |
66 gzip -c '${file}' > '${i}.gz' && | 125 gzip -c '${file}' > '${i}.gz' && |
67 #else | 126 #else |
68 ln -s '${file}' '${i}.gz' && | 127 ln -s '${file}' '${i}.gz' && |
69 #end if | 128 #end if |
70 #end for | 129 #end for |
80 #end if | 139 #end if |
81 #if $function_select.flank: | 140 #if $function_select.flank: |
82 -l $function_select.flank | 141 -l $function_select.flank |
83 #end if | 142 #end if |
84 $function_select.primary_alignments | 143 $function_select.primary_alignments |
144 | |
85 #for $i, $file in enumerate($function_select.input): | 145 #for $i, $file in enumerate($function_select.input): |
86 '${i}.gz' | 146 '${i}.gz' |
87 #end for | 147 #end for |
88 #else if $function_select.functions == "ngscstat": | 148 && mv PB.stat depth.stat |
149 && @CALCUTS@ depth.stat > cutoffs.tsv 2>calcuts.log | |
150 && @HIST_PLOT@ | |
151 | |
152 #else if $function_select.functions == 'ngscstat': | |
89 ngscstat | 153 ngscstat |
90 #if $function_select.min_align_qual: | 154 #if $function_select.min_align_qual: |
91 -q $function_select.min_align_qual | 155 -q $function_select.min_align_qual |
92 #end if | 156 #end if |
93 ## #if $function_select.max_depth: | 157 ## #if $function_select.max_depth: |
94 ## -M $function_select.max_depth | 158 ## -M $function_select.max_depth |
95 ## #end if | 159 ## #end if |
96 #if $function_select.max_insert: | 160 #if $function_select.max_insert: |
97 -L $function_select.max_insert | 161 -L $function_select.max_insert |
98 #end if | 162 #end if |
99 '$function_select.input' | 163 '${function_select.input}' |
100 #else if $function_select.functions == "calcuts": | 164 && mv TX.stat depth.stat |
101 calcuts | 165 && @CALCUTS@ depth.stat > cutoffs.tsv 2>calcuts.log |
102 #if $function_select.min_depth: | 166 && @HIST_PLOT@ |
103 -f $function_select.min_depth | 167 |
104 #end if | 168 #else if $function_select.functions == 'calcuts': |
105 #if $function_select.low_depth: | 169 @CALCUTS@ '${function_select.input}' > cutoffs.tsv 2>calcuts.log |
106 -l $function_select.low_depth | 170 |
107 #end if | 171 #else if $function_select.functions == 'get_seqs': |
108 #if $function_select.transition: | |
109 -m $function_select.transition | |
110 #end if | |
111 #if $function_select.upper_depth: | |
112 -u $function_select.upper_depth | |
113 #end if | |
114 $function_select.ploidy | |
115 '$function_select.input' > cutoffs.tsv 2>calcuts.log | |
116 #else if $function_select.functions == "get_seqs": | |
117 get_seqs | 172 get_seqs |
118 $function_select.coverage | 173 $function_select.coverage |
119 $function_select.haplotigs | 174 $function_select.haplotigs |
120 $function_select.end_trim | 175 $function_select.end_trim |
121 $function_select.split | 176 $function_select.split |
126 -m $function_select.min_ratio | 181 -m $function_select.min_ratio |
127 #end if | 182 #end if |
128 #if $function_select.min_gap: | 183 #if $function_select.min_gap: |
129 -g $function_select.min_gap | 184 -g $function_select.min_gap |
130 #end if | 185 #end if |
131 '$function_select.bed_input' '$function_select.fasta_input' | 186 '${function_select.bed_input}' '${function_select.fasta_input}' |
132 #end if | 187 #end if |
133 ]]></command> | 188 ]]></command> |
134 <inputs> | 189 <inputs> |
135 <conditional name="function_select"> | 190 <conditional name="function_select"> |
136 <param type="select" name="functions" label="Select the purge_dups function"> | 191 <param type="select" name="functions" label="Select the purge_dups function"> |
137 <option value="purge_dups">purge haplotigs and overlaps for an assembly</option> | 192 <option value="purge_dups">Purge haplotigs and overlaps for an assembly (purge_dups)</option> |
138 <option value="split_fa">split FASTA file by 'N's</option> | 193 <option value="split_fa">Split FASTA file by 'N's (split_fa)</option> |
139 <option value="pbcstat">create read depth histogram and base-level read depth for pacbio data</option> | 194 <option value="pbcstat">Calculate coverage cutoff and create read depth histogram and base-levelread depth for PacBio data (calcuts+pbcstats)</option> |
140 <option value="ngscstat">create read depth histogram and base-level read detph for illumina data</option> | 195 <option value="ngscstat">Calculate coverage cutoff and create read depth histogram and base-level read detph for Illumina data (calcuts+ngscstat)</option> |
141 <option value="calcuts">calculate coverage cutoffs</option> | 196 <option value="calcuts">calculate coverage cutoffs (calcuts)</option> |
142 <option value="get_seqs">obtain seqeuences after purging</option> | 197 <option value="get_seqs">Obtain seqeuences after purging (get_seqs)</option> |
143 </param> | 198 </param> |
144 <when value="purge_dups"> | 199 <when value="purge_dups"> |
145 <param name="input" type="data" format="paf,paf.gz" multiple="true" label="PAF input file"/> | 200 <param name="input" type="data" format="paf,paf.gz" multiple="true" label="PAF input file"/> |
146 <param name="coverage" type="data" format="tabular" optional="true" argument="-c" label="Base-level coverage file" /> | 201 <param name="coverage" type="data" format="tabular" optional="true" argument="-c" label="Base-level coverage file" /> |
147 <param name="cutoffs" type="data" format="tabular" label ="Cutoffs file" optional="true" argument="-T"/> | 202 <param name="cutoffs" type="data" format="tabular" label ="Cutoffs file" optional="true" argument="-T"/> |
172 <param name="max_cov" type="integer" label="Maximum coverage" argument="-M" optional="true"/> | 227 <param name="max_cov" type="integer" label="Maximum coverage" argument="-M" optional="true"/> |
173 <param name="min_map_ratio" argument="-f" type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/> | 228 <param name="min_map_ratio" argument="-f" type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/> |
174 <param name="min_map_qual" type="integer" argument="-q" optional="true" label="Minimum mapping quality"/> | 229 <param name="min_map_qual" type="integer" argument="-q" optional="true" label="Minimum mapping quality"/> |
175 <param name="flank" type="integer" argument="-l" optional="true" label="Flanking space" /> | 230 <param name="flank" type="integer" argument="-l" optional="true" label="Flanking space" /> |
176 <param name="primary_alignments" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Use only primary alignments" /> | 231 <param name="primary_alignments" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Use only primary alignments" /> |
232 <expand macro="calcuts" /> | |
233 <expand macro="trimmers"/> | |
177 </when> | 234 </when> |
178 <when value="ngscstat"> | 235 <when value="ngscstat"> |
179 <param name="input" type="data" format="bam" label="BAM input file"/> | 236 <param name="input" type="data" format="bam" label="BAM input file"/> |
180 <param name="min_align_qual" type="integer" argument="-q" optional="true" label="Minimum alignment quality" /> | 237 <param name="min_align_qual" type="integer" argument="-q" optional="true" label="Minimum alignment quality" /> |
181 <!-- Param exists in help text, but isn't actually part of the code. Maybe in the next release? --> | 238 <!-- Param exists in help text, but isn't actually part of the code. Maybe in the next release? --> |
182 <!-- <param name="max_depth" type="integer" label="Maximum read depth" argument="-M" optional="true"/> --> | 239 <!-- <param name="max_depth" type="integer" label="Maximum read depth" argument="-M" optional="true"/> --> |
183 <param name="max_insert" type="integer" argument="-L" optional="true" label="Maximum insert size"/> | 240 <param name="max_insert" type="integer" argument="-L" optional="true" label="Maximum insert size"/> |
241 <expand macro="calcuts" /> | |
242 <expand macro="trimmers"/> | |
184 </when> | 243 </when> |
244 | |
185 <when value="calcuts"> | 245 <when value="calcuts"> |
186 <param name="input" type="data" format="tabular" label="STAT input file"/> | 246 <param name="input" type="data" format="tabular" label="STAT input file"/> |
187 <param name="min_depth" type="float" label="Minimum depth count fraction to maximum depth coun" min="0" max="1" argument="-f" optional="true" help="Default = 0.1"/> | 247 <expand macro="calcuts" /> |
188 <param name="low_depth" label="Lower bound for read depth" type="integer" argument="-l" optional="true"/> | |
189 <param name="transition" label="Transition between haploid and diploid" type="integer" argument="-m" optional="true"/> | |
190 <param name="upper_depth" label="Upper bound for read depth" type="integer" argument="-u" optional="true"/> | |
191 <param name="ploidy" argument="-d" type="select" label="Ploidy"> | |
192 <option value="-d 0" selected="true">Diploid [0]</option> | |
193 <option value="-d 1">Haploid [1]</option> | |
194 </param> | |
195 </when> | 248 </when> |
249 | |
196 <when value="get_seqs"> | 250 <when value="get_seqs"> |
197 <param name="fasta_input" type="data" format="fasta" label="Fasta input file"/> | 251 <param name="fasta_input" type="data" format="fasta" label="Fasta input file"/> |
198 <param name="bed_input" type="data" format="bed" label="Bed input file"/> | 252 <param name="bed_input" type="data" format="bed" label="Bed input file"/> |
199 <param name="coverage" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Keep high coverage contigs in the primary contig set"/> | 253 <param name="coverage" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Keep high coverage contigs in the primary contig set"/> |
200 <param name="haplotigs" type="boolean" argument="-a" truevalue="-a" falsevalue="" checked="false" label="Do not add prefix to haplotigs"/> | 254 <param name="haplotigs" type="boolean" argument="-a" truevalue="-a" falsevalue="" checked="false" label="Do not add prefix to haplotigs"/> |
220 </data> | 274 </data> |
221 <!-- Ngscstat --> | 275 <!-- Ngscstat --> |
222 <data name="ngscstat_cov" format="tabular" from_work_dir="TX.base.cov" label="${tool.name} on ${on_string}: ngscstat base coverage file"> | 276 <data name="ngscstat_cov" format="tabular" from_work_dir="TX.base.cov" label="${tool.name} on ${on_string}: ngscstat base coverage file"> |
223 <filter>function_select['functions'] == 'ngscstat'</filter> | 277 <filter>function_select['functions'] == 'ngscstat'</filter> |
224 </data> | 278 </data> |
225 <data name="ngscstat_stat" format="tabular" from_work_dir="TX.stat" label="${tool.name} on ${on_string}: ngscstat stat file"> | 279 <data name="stat_file" format="tabular" from_work_dir="depth.stat" label="${tool.name} on ${on_string}: stat file"> |
226 <filter>function_select['functions'] == 'ngscstat'</filter> | 280 <filter>function_select['functions'] == 'ngscstat' or function_select['functions'] == 'pbcstat'</filter> |
227 </data> | 281 </data> |
228 <!-- Pbcstat --> | 282 <!-- Pbcstat --> |
229 <data name="pbcstat_cov" format="tabular" from_work_dir="PB.base.cov" label="${tool.name} on ${on_string}: pbcstat base coverage file"> | 283 <data name="pbcstat_cov" format="tabular" from_work_dir="PB.base.cov" label="${tool.name} on ${on_string}: pbcstat base coverage file"> |
230 <filter>function_select['functions'] == 'pbcstat'</filter> | 284 <filter>function_select['functions'] == 'pbcstat'</filter> |
231 </data> | 285 </data> |
232 <data name="pbcstat_wig" format="wig" from_work_dir="PB.cov.wig" label="${tool.name} on ${on_string}: pbcstat base wig file"> | 286 <data name="pbcstat_wig" format="wig" from_work_dir="PB.cov.wig" label="${tool.name} on ${on_string}: pbcstat base wig file"> |
233 <filter>function_select['functions'] == 'pbcstat'</filter> | 287 <filter>function_select['functions'] == 'pbcstat'</filter> |
234 </data> | 288 </data> |
235 <data name="pbcstat_stat" format="tabular" from_work_dir="PB.stat" label="${tool.name} on ${on_string}: stat file"> | 289 |
236 <filter>function_select['functions'] == 'pbcstat'</filter> | 290 <data name="hist" format="png" from_work_dir="hist.png" label="${tool.name} on ${on_string}: histogram plot"> |
237 </data> | 291 <filter>function_select['functions'] == 'pbcstat' or function_select['functions'] == 'ngscstat'</filter> |
292 </data> | |
293 | |
238 <!-- Calcuts --> | 294 <!-- Calcuts --> |
239 <data name="calcuts_log" format="txt" from_work_dir="calcuts.log" label="${tool.name} on ${on_string}: calcuts log file"> | 295 <data name="calcuts_log" format="txt" from_work_dir="calcuts.log" label="${tool.name} on ${on_string}: calcuts log file"> |
240 <filter>function_select['functions'] == 'calcuts'</filter> | 296 <filter>function_select['functions'] in ('pbcstat', 'ngscstat', 'calcuts')</filter> |
241 </data> | 297 </data> |
242 <data name="calcuts_tab" format="tabular" from_work_dir="cutoffs.tsv" label="${tool.name} on ${on_string}: calcuts cutoff file"> | 298 <data name="calcuts_tab" format="tabular" from_work_dir="cutoffs.tsv" label="${tool.name} on ${on_string}: calcuts cutoff file"> |
243 <filter>function_select['functions'] == 'calcuts'</filter> | 299 <filter>function_select['functions'] in ('pbcstat', 'ngscstat', 'calcuts')</filter> |
244 </data> | 300 </data> |
245 <!-- Purge dups --> | 301 <!-- Purge dups --> |
246 <data name="purge_dups_log" format="txt" from_work_dir="purge_dups.log" label="${tool.name} on ${on_string}: purge_dups log file"> | 302 <data name="purge_dups_log" format="txt" from_work_dir="purge_dups.log" label="${tool.name} on ${on_string}: purge_dups log file"> |
247 <filter>function_select['functions'] == 'purge_dups'</filter> | 303 <filter>function_select['functions'] == 'purge_dups'</filter> |
248 </data> | 304 </data> |
309 <param name="split" value="-n"/> | 365 <param name="split" value="-n"/> |
310 </conditional> | 366 </conditional> |
311 <output name="split_fasta" value="split_out.fasta"/> | 367 <output name="split_fasta" value="split_out.fasta"/> |
312 </test> | 368 </test> |
313 <!-- pbcstat --> | 369 <!-- pbcstat --> |
314 <test expect_num_outputs="3"> | 370 <test expect_num_outputs="6"> |
315 <conditional name="function_select"> | 371 <conditional name="function_select"> |
316 <param name="functions" value="pbcstat"/> | 372 <param name="functions" value="pbcstat"/> |
317 <param name="input" value="test.paf"/> | 373 <param name="input" value="test.paf"/> |
318 <param name="max_cov" value="1000"/> | 374 <param name="max_cov" value="1000"/> |
319 <param name="min_map_ratio" value="0.01"/> | 375 <param name="min_map_ratio" value="0.01"/> |
320 <param name="min_map_qual" value="1"/> | 376 <param name="min_map_qual" value="1"/> |
321 <param name="flank" value="1"/> | 377 <param name="flank" value="1"/> |
322 <param name="primary_alignments" value="-p"/> | 378 <param name="primary_alignments" value="-p"/> |
323 </conditional> | 379 <section name="section_calcuts"> |
380 <param name="min_depth" value="0.01"/> | |
381 <param name="low_depth" value="1"/> | |
382 <param name="transition" value="1"/> | |
383 <param name="upper_depth" value="100"/> | |
384 <param name="ploidy" value="-d 0"/> | |
385 </section> | |
386 </conditional> | |
387 <output name="calcuts_tab" value="calcuts_out.tsv"/> | |
324 <output name="pbcstat_cov" value="out.cov"/> | 388 <output name="pbcstat_cov" value="out.cov"/> |
325 <output name="pbcstat_wig" value="out.wig"/> | 389 <output name="pbcstat_wig" value="out.wig"/> |
390 <output name="stat_file" value="pbcstats.tabular"/> | |
391 <output name="hist" value="hist.png" ftype="png" compare="sim_size"/> | |
326 </test> | 392 </test> |
327 <!-- pbcstat gzip --> | 393 <!-- pbcstat gzip --> |
328 <test expect_num_outputs="3"> | 394 <test expect_num_outputs="6"> |
329 <conditional name="function_select"> | 395 <conditional name="function_select"> |
330 <param name="functions" value="pbcstat"/> | 396 <param name="functions" value="pbcstat"/> |
331 <param name="input" value="test.paf.gz" ftype="paf.gz"/> | 397 <param name="input" value="test.paf.gz" ftype="paf.gz"/> |
332 <param name="max_cov" value="1000"/> | 398 <param name="max_cov" value="1000"/> |
333 <param name="min_map_ratio" value="0.01"/> | 399 <param name="min_map_ratio" value="0.01"/> |
334 <param name="min_map_qual" value="1"/> | 400 <param name="min_map_qual" value="1"/> |
335 <param name="flank" value="1"/> | 401 <param name="flank" value="1"/> |
336 <param name="primary_alignments" value="-p"/> | 402 <param name="primary_alignments" value="-p"/> |
337 </conditional> | 403 <section name="section_calcuts"> |
404 <param name="min_depth" value="0.01"/> | |
405 <param name="low_depth" value="1"/> | |
406 <param name="transition" value="1"/> | |
407 <param name="upper_depth" value="100"/> | |
408 <param name="ploidy" value="-d 0"/> | |
409 </section> | |
410 </conditional> | |
411 <output name="calcuts_tab" value="calcuts_out.tsv"/> | |
338 <output name="pbcstat_cov" value="out.cov"/> | 412 <output name="pbcstat_cov" value="out.cov"/> |
339 <output name="pbcstat_wig" value="out.wig"/> | 413 <output name="pbcstat_wig" value="out.wig"/> |
340 </test> | 414 </test> |
341 <!-- Pbcstat multiple input --> | 415 <!-- Pbcstat multiple input --> |
342 <test expect_num_outputs="3"> | 416 <test expect_num_outputs="6"> |
343 <conditional name="function_select"> | 417 <conditional name="function_select"> |
344 <param name="functions" value="pbcstat"/> | 418 <param name="functions" value="pbcstat"/> |
345 <param name="input" value="test.paf,test2.paf.gz"/> | 419 <param name="input" value="test.paf,test2.paf.gz"/> |
346 </conditional> | 420 <section name="section_calcuts"> |
421 <param name="min_depth" value="0.01"/> | |
422 <param name="low_depth" value="1"/> | |
423 <param name="transition" value="1"/> | |
424 <param name="upper_depth" value="100"/> | |
425 <param name="ploidy" value="-d 0"/> | |
426 </section> | |
427 </conditional> | |
428 <output name="calcuts_tab" value="calcuts_out.tsv"/> | |
347 <output name="pbcstat_cov" value="out2.cov"/> | 429 <output name="pbcstat_cov" value="out2.cov"/> |
348 <output name="pbcstat_wig" value="out2.wig"/> | 430 <output name="stat_file" value="pbcstats2.tabular"/> |
431 <output name="pbcstat_wig" value="out2.wig"/> | |
349 </test> | 432 </test> |
350 <!-- ngscstat --> | 433 <!-- ngscstat --> |
351 <test expect_num_outputs="2"> | 434 <test expect_num_outputs="5"> |
352 <conditional name="function_select"> | 435 <conditional name="function_select"> |
353 <param name="functions" value="ngscstat"/> | 436 <param name="functions" value="ngscstat"/> |
354 <param name="input" value="test.bam"/> | 437 <param name="input" value="test.bam"/> |
355 <param name="min_align_qual" value="10"/> | 438 <param name="min_align_qual" value="10"/> |
356 <param name="max_insert" value="100"/> | 439 <param name="max_insert" value="100"/> |
357 </conditional> | 440 <section name="section_calcuts"> |
441 <param name="min_depth" value="0.01"/> | |
442 <param name="low_depth" value="1"/> | |
443 <param name="transition" value="1"/> | |
444 <param name="upper_depth" value="100"/> | |
445 <param name="ploidy" value="-d 0"/> | |
446 </section> | |
447 </conditional> | |
448 <output name="calcuts_tab" value="calcuts_out.tsv"/> | |
358 <output name="ngscstat_cov" value="ngsc_out.cov"/> | 449 <output name="ngscstat_cov" value="ngsc_out.cov"/> |
450 <output name="stat_file" value="tx_stats.tabular"/> | |
451 <output name="hist" value="hist.png" ftype="png" compare="sim_size"/> | |
359 </test> | 452 </test> |
360 <!-- Calcuts --> | 453 <!-- Calcuts --> |
361 <test expect_num_outputs="2"> | 454 <test expect_num_outputs="2"> |
362 <conditional name="function_select"> | 455 <conditional name="function_select"> |
363 <param name="functions" value="calcuts"/> | 456 <param name="functions" value="calcuts"/> |
364 <param name="input" value="test.stat"/> | 457 <param name="input" value="test.stat"/> |
365 <param name="min_depth" value="0.01"/> | 458 <section name="section_calcuts"> |
366 <param name="low_depth" value="1"/> | 459 <param name="min_depth" value="0.01"/> |
367 <param name="transition" value="1"/> | 460 <param name="low_depth" value="1"/> |
368 <param name="upper_depth" value="100"/> | 461 <param name="transition" value="1"/> |
369 <param name="ploidy" value="-d 0"/> | 462 <param name="upper_depth" value="100"/> |
463 <param name="ploidy" value="-d 0"/> | |
464 </section> | |
370 </conditional> | 465 </conditional> |
371 <output name="calcuts_tab" value="calcuts_out.tsv"/> | 466 <output name="calcuts_tab" value="calcuts_out.tsv"/> |
372 </test> | 467 </test> |
373 <!-- Get seqs --> | 468 <!-- Get seqs --> |
374 <test expect_num_outputs="2"> | 469 <test expect_num_outputs="2"> |
384 <param name="split" value="-s"/> | 479 <param name="split" value="-s"/> |
385 <param name="min_gap" value="100000"/> | 480 <param name="min_gap" value="100000"/> |
386 </conditional> | 481 </conditional> |
387 <output name="get_seqs_purged" value="purged_out.fa"/> | 482 <output name="get_seqs_purged" value="purged_out.fa"/> |
388 </test> | 483 </test> |
484 <!-- pbcstat histogram options--> | |
485 <test expect_num_outputs="6"> | |
486 <conditional name="function_select"> | |
487 <param name="functions" value="pbcstat"/> | |
488 <param name="input" value="test.paf"/> | |
489 <param name="max_cov" value="1000"/> | |
490 <param name="min_map_ratio" value="0.01"/> | |
491 <param name="min_map_qual" value="1"/> | |
492 <param name="flank" value="1"/> | |
493 <param name="primary_alignments" value="-p"/> | |
494 <section name="section_calcuts"> | |
495 <param name="min_depth" value="0.01"/> | |
496 <param name="low_depth" value="1"/> | |
497 <param name="transition" value="1"/> | |
498 <param name="upper_depth" value="100"/> | |
499 <param name="ploidy" value="-d 0"/> | |
500 </section> | |
501 <section name="section_hist"> | |
502 <param name="ymax" value="100"/> | |
503 <param name="xmax" value="100"/> | |
504 <param name="cutoffs_his" value="calcuts_out.tsv"/> | |
505 </section> | |
506 </conditional> | |
507 <output name="calcuts_tab" value="calcuts_out.tsv"/> | |
508 <output name="pbcstat_cov" value="out_hist_options.cov"/> | |
509 <output name="pbcstat_wig" value="out_hist_options.wig"/> | |
510 <output name="stat_file" value="pbcstats_hist_options.tabular"/> | |
511 <output name="hist" value="hist_options.png" ftype="png" compare="sim_size"/> | |
512 </test> | |
389 </tests> | 513 </tests> |
390 <help><![CDATA[ | 514 <help><![CDATA[ |
391 .. class:: infomark | 515 .. class:: infomark |
392 | 516 |
393 **What it does** | 517 **What it does** |