Mercurial > repos > iuc > purge_dups

comparison purge_dups.xml @ 2:17b378303f2d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
author iuc
date Tue, 27 Apr 2021 20:48:51 +0000
parents 29151e779524
children 76d4cbefff85
comparison
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1:29151e779524 2:17b378303f2d
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@">1</token> 5 <token name="@VERSION_SUFFIX@">2</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"): 12 #for $i, $file in enumerate($function_select.input):
13 gzip -c '$function_select.input' > ./input.paf.gz && 13 #if $file.is_of_type("paf"):
14 #end if 14 gzip -c '${file}' > '${i}.gz' &&
15 #else
16 ln -s '${file}' '${i}.gz' &&
17 #end if
18 #end for
15 purge_dups 19 purge_dups
16 #if $function_select.coverage: 20 #if $function_select.coverage:
17 -c '$function_select.coverage' 21 -c '$function_select.coverage'
18 #end if 22 #end if
19 #if $function_select.cutoffs: 23 #if $function_select.cutoffs:
44 -l $function_select.min_chain_score 48 -l $function_select.min_chain_score
45 #end if 49 #end if
46 #if $function_select.max_extend: 50 #if $function_select.max_extend:
47 -E $function_select.max_extend 51 -E $function_select.max_extend
48 #end if 52 #end if
49 #if $function_select.input.is_of_type("paf"): 53 #for $i, $file in enumerate($function_select.input):
50 'input.paf.gz' > dups.bed 2> purge_dups.log 54 '${i}.gz'
51 #else: 55 #end for
52 '${function_select.input}' > dups.bed 2> purge_dups.log 56 > dups.bed 2> purge_dups.log
53 #end if
54 #else if $function_select.functions == "split_fa": 57 #else if $function_select.functions == "split_fa":
55 split_fa 58 split_fa
56 #if $function_select.split: 59 #if $function_select.split:
57 -n $function_select.split 60 -n $function_select.split
58 #end if 61 #end if
59 '$function_select.input' > split.fasta 62 '$function_select.input' > split.fasta
60 #else if $function_select.functions == "pbcstat": 63 #else if $function_select.functions == "pbcstat":
61 #if $function_select.input.is_of_type("paf"): 64 #for $i, $file in enumerate($function_select.input):
62 gzip -c '$function_select.input' > ./input.paf.gz && 65 #if $file.is_of_type("paf"):
63 #end if 66 gzip -c '${file}' > '${i}.gz' &&
67 #else
68 ln -s '${file}' '${i}.gz' &&
69 #end if
70 #end for
64 pbcstat 71 pbcstat
65 #if $function_select.max_cov: 72 #if $function_select.max_cov:
66 -M $function_select.max_cov 73 -M $function_select.max_cov
67 #end if 74 #end if
68 #if $function_select.min_map_ratio: 75 #if $function_select.min_map_ratio:
73 #end if 80 #end if
74 #if $function_select.flank: 81 #if $function_select.flank:
75 -l $function_select.flank 82 -l $function_select.flank
76 #end if 83 #end if
77 $function_select.primary_alignments 84 $function_select.primary_alignments
78 #if $function_select.input.is_of_type("paf"): 85 #for $i, $file in enumerate($function_select.input):
79 'input.paf.gz' 86 '${i}.gz'
80 #else: 87 #end for
81 '${function_select.input}'
82 #end if
83 #else if $function_select.functions == "ngscstat": 88 #else if $function_select.functions == "ngscstat":
84 ngscstat 89 ngscstat
85 #if $function_select.min_align_qual: 90 #if $function_select.min_align_qual:
86 -q $function_select.min_align_qual 91 -q $function_select.min_align_qual
87 #end if 92 #end if
135 <option value="ngscstat">create read depth histogram and base-level read detph for illumina data</option> 140 <option value="ngscstat">create read depth histogram and base-level read detph for illumina data</option>
136 <option value="calcuts">calculate coverage cutoffs</option> 141 <option value="calcuts">calculate coverage cutoffs</option>
137 <option value="get_seqs">obtain seqeuences after purging</option> 142 <option value="get_seqs">obtain seqeuences after purging</option>
138 </param> 143 </param>
139 <when value="purge_dups"> 144 <when value="purge_dups">
140 <param name="input" type="data" format="paf,paf.gz" label="PAF input file"/> 145 <param name="input" type="data" format="paf,paf.gz" multiple="true" label="PAF input file"/>
141 <param name="coverage" type="data" format="tabular" optional="true" argument="-c" label="Base-level coverage file" /> 146 <param name="coverage" type="data" format="tabular" optional="true" argument="-c" label="Base-level coverage file" />
142 <param name="cutoffs" type="data" format="tabular" label ="Cutoffs file" optional="true" argument="-T"/> 147 <param name="cutoffs" type="data" format="tabular" label ="Cutoffs file" optional="true" argument="-T"/>
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"/> 148 <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"/>
144 <param name="min_align" type="integer" label="Minimum alignment score" argument="-a" optional="true"/> 149 <param name="min_align" type="integer" label="Minimum alignment score" argument="-a" optional="true"/>
145 <param name="min_match" type="integer" label="Minimum max match score" argument="-b" optional="true"/> 150 <param name="min_match" type="integer" label="Minimum max match score" argument="-b" optional="true"/>
161 <when value="split_fa"> 166 <when value="split_fa">
162 <param name="input" type="data" format="fasta" label="Base-level coverage file"/> 167 <param name="input" type="data" format="fasta" label="Base-level coverage file"/>
163 <param name="split" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Base-level coverage file" /> 168 <param name="split" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Base-level coverage file" />
164 </when> 169 </when>
165 <when value="pbcstat"> 170 <when value="pbcstat">
166 <param name="input" type="data" format="paf,paf.gz" label="PAF input file"/> 171 <param name="input" type="data" format="paf,paf.gz" multiple="true" label="PAF input file"/>
167 <param name="max_cov" type="integer" label="Maximum coverage" argument="-M" optional="true"/> 172 <param name="max_cov" type="integer" label="Maximum coverage" argument="-M" optional="true"/>
168 <param name="min_map_ratio" argument="-f" type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/> 173 <param name="min_map_ratio" argument="-f" type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/>
169 <param name="min_map_qual" type="integer" argument="-q" optional="true" label="Minimum mapping quality"/> 174 <param name="min_map_qual" type="integer" argument="-q" optional="true" label="Minimum mapping quality"/>
170 <param name="flank" type="integer" argument="-l" optional="true" label="Flanking space" /> 175 <param name="flank" type="integer" argument="-l" optional="true" label="Flanking space" />
171 <param name="primary_alignments" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Use only primary alignments" /> 176 <param name="primary_alignments" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Use only primary alignments" />
286 <param name="min_chain_score" value="1"/> 291 <param name="min_chain_score" value="1"/>
287 <param name="max_extend" value="100"/> 292 <param name="max_extend" value="100"/>
288 </conditional> 293 </conditional>
289 <output name="purge_dups_bed" value="purge_dups_out.bed"/> 294 <output name="purge_dups_bed" value="purge_dups_out.bed"/>
290 </test> 295 </test>
296 <!-- Purge dups multiple input -->
297 <test expect_num_outputs="2">
298 <conditional name="function_select">
299 <param name="functions" value="purge_dups"/>
300 <param name="input" value="test.paf,test2.paf.gz"/>
301 </conditional>
302 <output name="purge_dups_bed" value="purge_dups_out_2.bed"/>
303 </test>
291 <!-- Split fa --> 304 <!-- Split fa -->
292 <test expect_num_outputs="1"> 305 <test expect_num_outputs="1">
293 <conditional name="function_select"> 306 <conditional name="function_select">
294 <param name="functions" value="split_fa"/> 307 <param name="functions" value="split_fa"/>
295 <param name="input" value="test.fasta"/> 308 <param name="input" value="test.fasta"/>
322 <param name="flank" value="1"/> 335 <param name="flank" value="1"/>
323 <param name="primary_alignments" value="-p"/> 336 <param name="primary_alignments" value="-p"/>
324 </conditional> 337 </conditional>
325 <output name="pbcstat_cov" value="out.cov"/> 338 <output name="pbcstat_cov" value="out.cov"/>
326 <output name="pbcstat_wig" value="out.wig"/> 339 <output name="pbcstat_wig" value="out.wig"/>
340 </test>
341 <!-- Pbcstat multiple input -->
342 <test expect_num_outputs="3">
343 <conditional name="function_select">
344 <param name="functions" value="pbcstat"/>
345 <param name="input" value="test.paf,test2.paf.gz"/>
346 </conditional>
347 <output name="pbcstat_cov" value="out2.cov"/>
348 <output name="pbcstat_wig" value="out2.wig"/>
327 </test> 349 </test>
328 <!-- ngscstat --> 350 <!-- ngscstat -->
329 <test expect_num_outputs="2"> 351 <test expect_num_outputs="2">
330 <conditional name="function_select"> 352 <conditional name="function_select">
331 <param name="functions" value="ngscstat"/> 353 <param name="functions" value="ngscstat"/>