Mercurial > repos > iuc > purge_dups

comparison purge_dups.xml @ 1:29151e779524 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
author iuc
date Tue, 09 Mar 2021 18:25:07 +0000
parents 8ec117da1796
children 17b378303f2d
comparison
equal deleted inserted replaced
0:8ec117da1796 1:29151e779524
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"/>