Mercurial > repos > iuc > purge_dups
comparison purge_dups.xml @ 1:29151e779524 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
author | iuc |
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date | Tue, 09 Mar 2021 18:25:07 +0000 |
parents | 8ec117da1796 |
children | 17b378303f2d |
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0:8ec117da1796 | 1:29151e779524 |
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1 <tool id="purge_dups" name="Purge haplotigs" 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 overlaps in an assembly based on read depth</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@">0</token> | 5 <token name="@VERSION_SUFFIX@">1</token> |
6 </macros> | 6 </macros> |
7 <requirements> | 7 <requirements> |
8 <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement> | 8 <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement> |
9 </requirements> | 9 </requirements> |
10 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
11 #if $function_select.functions == "purge_dups": | 11 #if $function_select.functions == "purge_dups": |
12 #if $function_select.input.is_of_type("paf"): | |
13 gzip -c '$function_select.input' > ./input.paf.gz && | |
14 #end if | |
12 purge_dups | 15 purge_dups |
13 #if $function_select.coverage: | 16 #if $function_select.coverage: |
14 -c '$function_select.coverage' | 17 -c '$function_select.coverage' |
15 #end if | 18 #end if |
16 #if $function_select.cutoffs: | 19 #if $function_select.cutoffs: |
41 -l $function_select.min_chain_score | 44 -l $function_select.min_chain_score |
42 #end if | 45 #end if |
43 #if $function_select.max_extend: | 46 #if $function_select.max_extend: |
44 -E $function_select.max_extend | 47 -E $function_select.max_extend |
45 #end if | 48 #end if |
46 '$function_select.input' > dups.bed 2> purge_dups.log | 49 #if $function_select.input.is_of_type("paf"): |
50 'input.paf.gz' > dups.bed 2> purge_dups.log | |
51 #else: | |
52 '${function_select.input}' > dups.bed 2> purge_dups.log | |
53 #end if | |
47 #else if $function_select.functions == "split_fa": | 54 #else if $function_select.functions == "split_fa": |
48 split_fa | 55 split_fa |
49 #if $function_select.split: | 56 #if $function_select.split: |
50 -n $function_select.split | 57 -n $function_select.split |
51 #end if | 58 #end if |
52 '$function_select.input' > split.fasta | 59 '$function_select.input' > split.fasta |
53 #else if $function_select.functions == "pbcstat": | 60 #else if $function_select.functions == "pbcstat": |
61 #if $function_select.input.is_of_type("paf"): | |
62 gzip -c '$function_select.input' > ./input.paf.gz && | |
63 #end if | |
54 pbcstat | 64 pbcstat |
55 #if $function_select.max_cov: | 65 #if $function_select.max_cov: |
56 -M $function_select.max_cov | 66 -M $function_select.max_cov |
57 #end if | 67 #end if |
58 #if $function_select.min_map_ratio: | 68 #if $function_select.min_map_ratio: |
63 #end if | 73 #end if |
64 #if $function_select.flank: | 74 #if $function_select.flank: |
65 -l $function_select.flank | 75 -l $function_select.flank |
66 #end if | 76 #end if |
67 $function_select.primary_alignments | 77 $function_select.primary_alignments |
68 '$function_select.input' | 78 #if $function_select.input.is_of_type("paf"): |
79 'input.paf.gz' | |
80 #else: | |
81 '${function_select.input}' | |
82 #end if | |
69 #else if $function_select.functions == "ngscstat": | 83 #else if $function_select.functions == "ngscstat": |
70 ngscstat | 84 ngscstat |
71 #if $function_select.min_align_qual: | 85 #if $function_select.min_align_qual: |
72 -q $function_select.min_align_qual | 86 -q $function_select.min_align_qual |
73 #end if | 87 #end if |
121 <option value="ngscstat">create read depth histogram and base-level read detph for illumina data</option> | 135 <option value="ngscstat">create read depth histogram and base-level read detph for illumina data</option> |
122 <option value="calcuts">calculate coverage cutoffs</option> | 136 <option value="calcuts">calculate coverage cutoffs</option> |
123 <option value="get_seqs">obtain seqeuences after purging</option> | 137 <option value="get_seqs">obtain seqeuences after purging</option> |
124 </param> | 138 </param> |
125 <when value="purge_dups"> | 139 <when value="purge_dups"> |
126 <param name="input" type="data" format="paf" label="PAF input file"/> | 140 <param name="input" type="data" format="paf,paf.gz" label="PAF input file"/> |
127 <param name="coverage" type="data" format="tabular" optional="true" argument="-c" label="Base-level coverage file" /> | 141 <param name="coverage" type="data" format="tabular" optional="true" argument="-c" label="Base-level coverage file" /> |
128 <param name="cutoffs" type="data" format="tabular" label ="Cutoffs file" optional="true" argument="-T"/> | 142 <param name="cutoffs" type="data" format="tabular" label ="Cutoffs file" optional="true" argument="-T"/> |
129 <param name="min_bad" type="float" min="0" max="1" argument="-f" optional="true" label="Minimum fraction of haploid/diploid/bad/repetitive bases in a sequence" help="Default = 0.8"/> | 143 <param name="min_bad" type="float" min="0" max="1" argument="-f" optional="true" label="Minimum fraction of haploid/diploid/bad/repetitive bases in a sequence" help="Default = 0.8"/> |
130 <param name="min_align" type="integer" label="Minimum alignment score" argument="-a" optional="true"/> | 144 <param name="min_align" type="integer" label="Minimum alignment score" argument="-a" optional="true"/> |
131 <param name="min_match" type="integer" label="Minimum max match score" argument="-b" optional="true"/> | 145 <param name="min_match" type="integer" label="Minimum max match score" argument="-b" optional="true"/> |
147 <when value="split_fa"> | 161 <when value="split_fa"> |
148 <param name="input" type="data" format="fasta" label="Base-level coverage file"/> | 162 <param name="input" type="data" format="fasta" label="Base-level coverage file"/> |
149 <param name="split" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Base-level coverage file" /> | 163 <param name="split" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Base-level coverage file" /> |
150 </when> | 164 </when> |
151 <when value="pbcstat"> | 165 <when value="pbcstat"> |
152 <param name="input" type="data" format="paf" label="PAF input file"/> | 166 <param name="input" type="data" format="paf,paf.gz" label="PAF input file"/> |
153 <param name="max_cov" type="integer" label="Maximum coverage" argument="-M" optional="true"/> | 167 <param name="max_cov" type="integer" label="Maximum coverage" argument="-M" optional="true"/> |
154 <param name="min_map_ratio" argument="-f" type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/> | 168 <param name="min_map_ratio" argument="-f" type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/> |
155 <param name="min_map_qual" type="integer" argument="-q" optional="true" label="Minimum mapping quality"/> | 169 <param name="min_map_qual" type="integer" argument="-q" optional="true" label="Minimum mapping quality"/> |
156 <param name="flank" type="integer" argument="-l" optional="true" label="Flanking space" /> | 170 <param name="flank" type="integer" argument="-l" optional="true" label="Flanking space" /> |
157 <param name="primary_alignments" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Use only primary alignments" /> | 171 <param name="primary_alignments" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Use only primary alignments" /> |
251 <param name="min_chain_score" value="1"/> | 265 <param name="min_chain_score" value="1"/> |
252 <param name="max_extend" value="100"/> | 266 <param name="max_extend" value="100"/> |
253 </conditional> | 267 </conditional> |
254 <output name="purge_dups_bed" value="purge_dups_out.bed"/> | 268 <output name="purge_dups_bed" value="purge_dups_out.bed"/> |
255 </test> | 269 </test> |
270 <!-- Purge dups gzip --> | |
271 <test expect_num_outputs="2"> | |
272 <conditional name="function_select"> | |
273 <param name="functions" value="purge_dups"/> | |
274 <param name="input" value="test.paf.gz" ftype="paf.gz"/> | |
275 <param name="coverage" value="test.cov" ftype="tabular"/> | |
276 <param name="cutoffs" value="cutoffs.tsv" ftype="tabular"/> | |
277 <param name="min_bad" value="0.01"/> | |
278 <param name="min_align" value="10"/> | |
279 <param name="min_match" value="100"/> | |
280 <param name="min_chain" value="1"/> | |
281 <param name="max_gap" value="1000"/> | |
282 <conditional name="double_chain"> | |
283 <param name="chaining_rounds" value="two"/> | |
284 <param name="max_gap_2" value="1001"/> | |
285 </conditional> | |
286 <param name="min_chain_score" value="1"/> | |
287 <param name="max_extend" value="100"/> | |
288 </conditional> | |
289 <output name="purge_dups_bed" value="purge_dups_out.bed"/> | |
290 </test> | |
256 <!-- Split fa --> | 291 <!-- Split fa --> |
257 <test expect_num_outputs="1"> | 292 <test expect_num_outputs="1"> |
258 <conditional name="function_select"> | 293 <conditional name="function_select"> |
259 <param name="functions" value="split_fa"/> | 294 <param name="functions" value="split_fa"/> |
260 <param name="input" value="test.fasta"/> | 295 <param name="input" value="test.fasta"/> |
265 <!-- pbcstat --> | 300 <!-- pbcstat --> |
266 <test expect_num_outputs="3"> | 301 <test expect_num_outputs="3"> |
267 <conditional name="function_select"> | 302 <conditional name="function_select"> |
268 <param name="functions" value="pbcstat"/> | 303 <param name="functions" value="pbcstat"/> |
269 <param name="input" value="test.paf"/> | 304 <param name="input" value="test.paf"/> |
305 <param name="max_cov" value="1000"/> | |
306 <param name="min_map_ratio" value="0.01"/> | |
307 <param name="min_map_qual" value="1"/> | |
308 <param name="flank" value="1"/> | |
309 <param name="primary_alignments" value="-p"/> | |
310 </conditional> | |
311 <output name="pbcstat_cov" value="out.cov"/> | |
312 <output name="pbcstat_wig" value="out.wig"/> | |
313 </test> | |
314 <!-- pbcstat gzip --> | |
315 <test expect_num_outputs="3"> | |
316 <conditional name="function_select"> | |
317 <param name="functions" value="pbcstat"/> | |
318 <param name="input" value="test.paf.gz" ftype="paf.gz"/> | |
270 <param name="max_cov" value="1000"/> | 319 <param name="max_cov" value="1000"/> |
271 <param name="min_map_ratio" value="0.01"/> | 320 <param name="min_map_ratio" value="0.01"/> |
272 <param name="min_map_qual" value="1"/> | 321 <param name="min_map_qual" value="1"/> |
273 <param name="flank" value="1"/> | 322 <param name="flank" value="1"/> |
274 <param name="primary_alignments" value="-p"/> | 323 <param name="primary_alignments" value="-p"/> |