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comparison spades.xml @ 10:b8d633fbf5f5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9
author iuc
date Tue, 11 Dec 2018 13:36:00 -0500
parents 24fffa4fee40
children 1796ea206dec
comparison
equal deleted inserted replaced
9:24fffa4fee40 10:b8d633fbf5f5
1 <tool id="spades" name="SPAdes" version="@TOOL_VERSION@"> 1 <tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy1">
2 <description>genome assembler for regular and single-cell projects</description> 2 <description>genome assembler for regular and single-cell projects</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
18 description="Out of memory error occurred" /> 18 description="Out of memory error occurred" />
19 </stdio> 19 </stdio>
20 <command> 20 <command>
21 <![CDATA[ 21 <![CDATA[
22 ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output 22 ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output
23 23
24 if [[ -n \$GALAXY_MEMORY_MB ]]; then 24 if [[ -n \$GALAXY_MEMORY_MB ]]; then
25 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 )); 25 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
26 fi && 26 fi &&
27 27
28 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250} 28 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250}
47 #set prefix = 'hqmp' 47 #set prefix = 'hqmp'
48 #end if 48 #end if
49 --$prefix$i-$library.orientation 49 --$prefix$i-$library.orientation
50 #for $file in $library.files 50 #for $file in $library.files
51 #if $file.file_type.type == "separate" 51 #if $file.file_type.type == "separate"
52 --$prefix$i-1 $file.file_type.fwd_reads.extension:$file.file_type.fwd_reads 52 --$prefix$i-1 $file.file_type.fwd_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.fwd_reads
53 --$prefix$i-2 $file.file_type.fwd_reads.extension:$file.file_type.rev_reads 53 --$prefix$i-2 $file.file_type.fwd_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.rev_reads
54 #elif $file.file_type.type == "interleaved" 54 #elif $file.file_type.type == "interleaved"
55 --$prefix$i-12 $file.file_type.interleaved_reads.extension:$file.file_type.interleaved_reads 55 --$prefix$i-12 $file.file_type.interleaved_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.interleaved_reads
56 #elif $file.file_type.type == "merged" 56 #elif $file.file_type.type == "merged"
57 --$prefix$i-m $file.file_type.merged_reads.extension:$file.file_type.merged_reads 57 --$prefix$i-m $file.file_type.merged_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.merged_reads
58 #elif $file.file_type.type == "unpaired" 58 #elif $file.file_type.type == "unpaired"
59 --$prefix$i-s $file.file_type.unpaired_reads.extension:$file.file_type.unpaired_reads 59 --$prefix$i-s $file.file_type.unpaired_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.unpaired_reads
60 #elif $file.file_type.type == "paired-collection" 60 #elif $file.file_type.type == "paired-collection"
61 --$prefix$i-1 $file.file_type.fastq_collection.forward.extension:$file.file_type.fastq_collection.forward 61 --$prefix$i-1 $file.file_type.fastq_collection.forward.extension.replace('fastqsanger', 'fastq'):$file.file_type.fastq_collection.forward
62 --$prefix$i-2 $file.file_type.fastq_collection.reverse.extension:$file.file_type.fastq_collection.reverse 62 --$prefix$i-2 $file.file_type.fastq_collection.reverse.extension.replace('fastqsanger', 'fastq'):$file.file_type.fastq_collection.reverse
63 #end if 63 #end if
64 #end for 64 #end for
65 #end for 65 #end for
66 #for $read in $pacbio_reads: 66 #for $read in $pacbio_reads:
67 #if $read: 67 #if $read:
73 --nanopore fastq:$read 73 --nanopore fastq:$read
74 #end if 74 #end if
75 #end for 75 #end for
76 #for $read in $sanger_reads: 76 #for $read in $sanger_reads:
77 #if $read: 77 #if $read:
78 --sanger $read.extension:$read 78 --sanger $read.extension.replace('fastqsanger', 'fastq'):$read
79 #end if 79 #end if
80 #end for 80 #end for
81 #for $contig in $trusted_contigs: 81 #for $contig in $trusted_contigs:
82 #if $contig: 82 #if $contig:
83 --trusted-contigs $contig.extension:$contig 83 --trusted-contigs $contig.extension.replace('fastqsanger', 'fastq'):$contig
84 #end if 84 #end if
85 #end for 85 #end for
86 #for $contig in $untrusted_contigs: 86 #for $contig in $untrusted_contigs:
87 #if $contig: 87 #if $contig:
88 --untrusted-contigs $contig.extension:$contig 88 --untrusted-contigs $contig.extension.replace('fastqsanger', 'fastq'):$contig
89 #end if 89 #end if
90 #end for 90 #end for
91 && python '$write_tsv_script' < contigs.fasta > '$out_contig_stats' 91 && python '$write_tsv_script' < contigs.fasta > '$out_contig_stats'
92 && python '$write_tsv_script' < scaffolds.fasta > '$out_scaffold_stats' 92 && python '$write_tsv_script' < scaffolds.fasta > '$out_scaffold_stats'
93 ]]> 93 ]]>
94 </command> 94 </command>
95 95
96 <configfiles> 96 <configfiles>
97 <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python 97 <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python
98 import sys,re 98 import sys,re
99 search_str = r'^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$' 99 search_str = r'^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$'
100 replace_str = r'\1_\2\t\3\t\4' 100 replace_str = r'\1_\2\t\3\t\4'
104 if cmd.match(line): 104 if cmd.match(line):
105 sys.stdout.write(cmd.sub(replace_str,line)) 105 sys.stdout.write(cmd.sub(replace_str,line))
106 ]]> 106 ]]>
107 </configfile> 107 </configfile>
108 </configfiles> 108 </configfiles>
109 109
110 <inputs> 110 <inputs>
111 <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean"> 111 <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean">
112 <option value="false">No</option> 112 <option value="false">No</option>
113 <option value="true">Yes</option> 113 <option value="true">Yes</option>
114 </param> 114 </param>
115 <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" /> 115 <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" />
116 <param argument="----careful" checked="True" falsevalue="" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector &#8211; a post processing tool, which uses BWA tool (comes with SPAdes)." label="Careful correction?" name="careful" truevalue="--careful" type="boolean" /> 116 <param argument="--careful" checked="True" falsevalue="" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector &#8211; a post processing tool, which uses BWA tool (comes with SPAdes)." label="Careful correction?" name="careful" truevalue="--careful" type="boolean" />
117 <conditional name="kmer_choice"> 117 <conditional name="kmer_choice">
118 <param checked="False" falsevalue="false" help="k-mer choices can be chosen by SPAdes instead of being entered manually" label="Automatically choose k-mer values" name="auto_kmer_choice" truevalue="true" type="boolean" /> 118 <param checked="False" falsevalue="false" help="k-mer choices can be chosen by SPAdes instead of being entered manually" label="Automatically choose k-mer values" name="auto_kmer_choice" truevalue="true" type="boolean" />
119 <when value="false"> 119 <when value="false">
120 <param help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." label="K-mers to use, separated by commas" name="kmers" type="text" value="21,33,55" /> 120 <param help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." label="K-mers to use, separated by commas" name="kmers" type="text" value="21,33,55" />
121 </when> 121 </when>
217 <assert_contents> 217 <assert_contents>
218 <has_text_matching expression="NODE_1\t1000"/> 218 <has_text_matching expression="NODE_1\t1000"/>
219 </assert_contents> 219 </assert_contents>
220 </output> 220 </output>
221 </test> 221 </test>
222 <test> <!-- Test 1 - basic test with k=33 fasta input --> 222 <test> <!-- Test 2 - basic test with k=33 fasta input -->
223 <param name="sc" value="false" /> 223 <param name="sc" value="false" />
224 <param name="onlyassembler" value="true"/> 224 <param name="onlyassembler" value="true"/>
225 <param name="careful" value="false" /> 225 <param name="careful" value="false" />
226 <param name="kmers" value="33" /> 226 <param name="kmers" value="33" />
227 <param name="lib_type" value="paired_end" /> 227 <param name="lib_type" value="paired_end" />
232 <assert_contents> 232 <assert_contents>
233 <has_text_matching expression="NODE_1\t1000"/> 233 <has_text_matching expression="NODE_1\t1000"/>
234 </assert_contents> 234 </assert_contents>
235 </output> 235 </output>
236 </test> 236 </test>
237 <test> <!-- Test 1 - basic test with k=33 and gzipped input --> 237 <test> <!-- Test 3 - basic test with k=33 and gzipped input -->
238 <param name="sc" value="false" /> 238 <param name="sc" value="false" />
239 <param name="careful" value="false" /> 239 <param name="careful" value="false" />
240 <param name="kmers" value="33" /> 240 <param name="kmers" value="33" />
241 <param name="lib_type" value="paired_end" /> 241 <param name="lib_type" value="paired_end" />
242 <param ftype="fastq.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" /> 242 <param ftype="fastq.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" />
246 <assert_contents> 246 <assert_contents>
247 <has_text_matching expression="NODE_1\t1000"/> 247 <has_text_matching expression="NODE_1\t1000"/>
248 </assert_contents> 248 </assert_contents>
249 </output> 249 </output>
250 </test> 250 </test>
251 <test> <!-- Test 2 - auto k --> 251 <test> <!-- Test 4 - auto k -->
252 <param name="sc" value="false" /> 252 <param name="sc" value="false" />
253 <param name="careful" value="false" /> 253 <param name="careful" value="false" />
254 <param name="auto_kmer_choice" value="true" /> 254 <param name="auto_kmer_choice" value="true" />
255 <param name="lib_type" value="paired_end" /> 255 <param name="lib_type" value="paired_end" />
256 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> 256 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
257 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" /> 257 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
258 <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> 258 <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
259 </test> 259 </test>
260 <test> <!-- Test 3 - k=77 --> 260 <test> <!-- Test 5 - k=77 -->
261 <param name="sc" value="false" /> 261 <param name="sc" value="false" />
262 <param name="careful" value="false" /> 262 <param name="careful" value="false" />
263 <param name="kmers" value="77" /> 263 <param name="kmers" value="77" />
264 <param name="lib_type" value="paired_end" /> 264 <param name="lib_type" value="paired_end" />
265 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> 265 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
266 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" /> 266 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
267 <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> 267 <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
268 </test> 268 </test>
269 <test> <!-- Test 4 - test for extra graph outputs --> 269 <test> <!-- Test 6 - test for extra graph outputs -->
270 <param name="sc" value="false" /> 270 <param name="sc" value="false" />
271 <param name="careful" value="false" /> 271 <param name="careful" value="false" />
272 <param name="kmers" value="33" /> 272 <param name="kmers" value="33" />
273 <param name="lib_type" value="paired_end" /> 273 <param name="lib_type" value="paired_end" />
274 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> 274 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
287 </assert_contents> 287 </assert_contents>
288 </output> 288 </output>
289 <output name="scaffold_graph"> 289 <output name="scaffold_graph">
290 <assert_contents> 290 <assert_contents>
291 <has_text text="NODE_"/> 291 <has_text text="NODE_"/>
292 </assert_contents>
293 </output>
294 </test>
295 <test> <!-- Test 7 - basic test with k=33 and fastsanger input -->
296 <param name="sc" value="false" />
297 <param name="careful" value="false" />
298 <param name="kmers" value="33" />
299 <param name="lib_type" value="paired_end" />
300 <param ftype="fastqsanger" name="fwd_reads" value="ecoli_1K_1.fq" />
301 <param ftype="fastqsanger" name="rev_reads" value="ecoli_1K_2.fq" />
302 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
303 <output name="out_contig_stats">
304 <assert_contents>
305 <has_text_matching expression="NODE_1\t1000"/>
306 </assert_contents>
307 </output>
308 </test>
309 <test> <!-- Test 8 - basic test with k=33 and fastsanger.gz input -->
310 <param name="sc" value="false" />
311 <param name="careful" value="false" />
312 <param name="kmers" value="33" />
313 <param name="lib_type" value="paired_end" />
314 <param ftype="fastqsanger.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" />
315 <param ftype="fastqsanger.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" />
316 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
317 <output name="out_contig_stats">
318 <assert_contents>
319 <has_text_matching expression="NODE_1\t1000"/>
292 </assert_contents> 320 </assert_contents>
293 </output> 321 </output>
294 </test> 322 </test>
295 </tests> 323 </tests>
296 <help> 324 <help>