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comparison spades.xml @ 9:24fffa4fee40 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author iuc
date Tue, 30 Oct 2018 20:27:11 -0400
parents 884dc0264950
children b8d633fbf5f5
comparison
equal deleted inserted replaced
8:884dc0264950 9:24fffa4fee40
1 <tool id="spades" name="SPAdes" version="3.11.1+galaxy1"> 1 <tool id="spades" name="SPAdes" version="@TOOL_VERSION@">
2 <description>genome assembler for regular and single-cell projects</description> 2 <description>genome assembler for regular and single-cell projects</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="3.11.1">spades</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
5 </requirements> 8 </requirements>
6 <stdio> 9 <stdio>
7 <exit_code range="1:" /> 10 <exit_code range="1:" />
11 <regex match="Cannot allocate memory"
12 source="stdout"
13 level="fatal_oom"
14 description="Out of memory error occurred" />
8 <regex match="The reads contain too many k-mers to fit into available memory" 15 <regex match="The reads contain too many k-mers to fit into available memory"
9 source="stdout" 16 source="stdout"
10 level="fatal_oom" 17 level="fatal_oom"
11 description="Out of memory error occurred" /> 18 description="Out of memory error occurred" />
12 </stdio> 19 </stdio>
13 <command> 20 <command>
14 <![CDATA[ 21 <![CDATA[
15 ## 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
16 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16} 23
24 if [[ -n \$GALAXY_MEMORY_MB ]]; then
25 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
26 fi &&
27
28 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250}
17 #if not $kmer_choice.auto_kmer_choice: 29 #if not $kmer_choice.auto_kmer_choice:
18 -k "$kmer_choice.kmers" 30 -k "$kmer_choice.kmers"
19 #end if 31 #end if
20 #if $cov.state == "auto": 32 #if $cov.state == "auto":
21 --cov-cutoff 'auto' 33 --cov-cutoff 'auto'
35 #set prefix = 'hqmp' 47 #set prefix = 'hqmp'
36 #end if 48 #end if
37 --$prefix$i-$library.orientation 49 --$prefix$i-$library.orientation
38 #for $file in $library.files 50 #for $file in $library.files
39 #if $file.file_type.type == "separate" 51 #if $file.file_type.type == "separate"
40 --$prefix$i-1 fastq:$file.file_type.fwd_reads 52 --$prefix$i-1 $file.file_type.fwd_reads.extension:$file.file_type.fwd_reads
41 --$prefix$i-2 fastq:$file.file_type.rev_reads 53 --$prefix$i-2 $file.file_type.fwd_reads.extension:$file.file_type.rev_reads
42 #elif $file.file_type.type == "interleaved" 54 #elif $file.file_type.type == "interleaved"
43 --$prefix$i-12 fastq:$file.file_type.interleaved_reads 55 --$prefix$i-12 $file.file_type.interleaved_reads.extension:$file.file_type.interleaved_reads
56 #elif $file.file_type.type == "merged"
57 --$prefix$i-m $file.file_type.merged_reads.extension:$file.file_type.merged_reads
44 #elif $file.file_type.type == "unpaired" 58 #elif $file.file_type.type == "unpaired"
45 --$prefix$i-s fastq:$file.file_type.unpaired_reads 59 --$prefix$i-s $file.file_type.unpaired_reads.extension:$file.file_type.unpaired_reads
46 #elif $file.file_type.type == "paired-collection" 60 #elif $file.file_type.type == "paired-collection"
47 --$prefix$i-1 fastq:$file.file_type.fastq_collection.forward 61 --$prefix$i-1 $file.file_type.fastq_collection.forward.extension:$file.file_type.fastq_collection.forward
48 --$prefix$i-2 fastq:$file.file_type.fastq_collection.reverse 62 --$prefix$i-2 $file.file_type.fastq_collection.reverse.extension:$file.file_type.fastq_collection.reverse
49 #end if 63 #end if
50 #end for 64 #end for
51 #end for 65 #end for
52 #for $read in $pacbio_reads: 66 #for $read in $pacbio_reads:
53 #if $read: 67 #if $read:
72 #for $contig in $untrusted_contigs: 86 #for $contig in $untrusted_contigs:
73 #if $contig: 87 #if $contig:
74 --untrusted-contigs $contig.extension:$contig 88 --untrusted-contigs $contig.extension:$contig
75 #end if 89 #end if
76 #end for 90 #end for
77 && cat contigs.fasta | python '$write_tsv_script' > '$out_contig_stats' 91 && python '$write_tsv_script' < contigs.fasta > '$out_contig_stats'
78 && cat scaffolds.fasta | python '$write_tsv_script' > '$out_scaffold_stats' 92 && python '$write_tsv_script' < scaffolds.fasta > '$out_scaffold_stats'
79 ]]> 93 ]]>
80 </command> 94 </command>
81 95
82 <configfiles> 96 <configfiles>
83 <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python 97 <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python
118 <param help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" label="Coverage cutoff value" name="cutoff" type="float" value="" /> 132 <param help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" label="Coverage cutoff value" name="cutoff" type="float" value="" />
119 </when> 133 </when>
120 <when value="auto" /> 134 <when value="auto" />
121 </conditional> 135 </conditional>
122 <param checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" /> 136 <param checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" />
123 <repeat help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided." min="1" name="libraries" title="Libraries"> 137 <repeat help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided." min="1" max="9" name="libraries" title="Libraries">
124 <param label="Library type" name="lib_type" type="select"> 138 <param label="Library type" name="lib_type" type="select">
125 <option value="paired_end">Paired-end / Single reads</option> 139 <option value="paired_end">Paired-end / Single reads</option>
126 <option value="mate_paired">Mate pairs</option> 140 <option value="mate_paired">Mate pairs</option>
127 <option value="high_mate_paired">High Quality Mate pairs</option> 141 <option value="high_mate_paired">High Quality Mate pairs</option>
128 <option value="nxmate_paired">Lucigen NxMate pairs</option> 142 <option value="nxmate_paired">Lucigen NxMate pairs</option>
135 <repeat min="1" name="files" title="Files"> 149 <repeat min="1" name="files" title="Files">
136 <conditional name="file_type"> 150 <conditional name="file_type">
137 <param label="Select file format" name="type" type="select"> 151 <param label="Select file format" name="type" type="select">
138 <option value="separate">Separate input files</option> 152 <option value="separate">Separate input files</option>
139 <option value="interleaved">Interleaved files</option> 153 <option value="interleaved">Interleaved files</option>
154 <option value="merged">Merged files</option>
140 <option value="unpaired">Unpaired/Single reads</option> 155 <option value="unpaired">Unpaired/Single reads</option>
141 <option value="paired-collection">Paired List Collection</option> 156 <option value="paired-collection">Paired List Collection</option>
142 </param> 157 </param>
143 <when value="separate"> 158 <when value="separate">
144 <param format="fastq" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" /> 159 <param format="@INTYPES@" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" />
145 <param format="fastq" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" /> 160 <param format="@INTYPES@" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" />
146 </when> 161 </when>
147 <when value="interleaved"> 162 <when value="interleaved">
148 <param format="fastq" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" /> 163 <param format="@INTYPES@" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" />
164 </when>
165 <when value="merged">
166 <param format="@INTYPES@" help="FASTQ format" label="Merged paired reads" name="merged_reads" type="data" />
149 </when> 167 </when>
150 <when value="unpaired"> 168 <when value="unpaired">
151 <param format="fastq" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" /> 169 <param format="@INTYPES@" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" />
152 </when> 170 </when>
153 <when value="paired-collection"> 171 <when value="paired-collection">
154 <param collection_type="paired" format="fastq" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" /> 172 <param collection_type="paired" format="@INTYPES@" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" />
155 </when> 173 </when>
156 </conditional> 174 </conditional>
157 </repeat> 175 </repeat>
158 </repeat> 176 </repeat>
159 <param optional="true" format="fastq" label="PacBio CLR reads" multiple="true" name="pacbio_reads" type="data" /> 177 <param optional="true" format="@INTYPES@" label="PacBio CLR reads" multiple="true" name="pacbio_reads" type="data" />
160 <param optional="true" format="fastq" label="Nanopore reads" multiple="true" name="nanopore_reads" type="data" /> 178 <param optional="true" format="@INTYPES@" label="Nanopore reads" multiple="true" name="nanopore_reads" type="data" />
161 <param optional="true" format="fasta,fastq" label="Sanger reads" multiple="true" name="sanger_reads" type="data" /> 179 <param optional="true" format="@INTYPES@" label="Sanger reads" multiple="true" name="sanger_reads" type="data" />
162 <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" /> 180 <param optional="true" format="@INTYPES@" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
163 <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" /> 181 <param optional="true" format="@INTYPES@" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
164 <param name="contig_graph_out" type="boolean" checked="False" label="Output final assembly graph (contigs)?" help="Will output the final assembly graph (contigs) in fastg format for visualisation" /> 182 <param name="contig_graph_out" type="boolean" checked="False" label="Output final assembly graph (contigs)?" help="Will output the final assembly graph (contigs) in fastg format for visualisation" />
165 <param name="scaffold_graph_out" type="boolean" checked="False" label="Output final assembly graph with scaffolds?" help="Will output the final assembly graph with scaffold information in gfa format for visualisation" /> 183 <param name="scaffold_graph_out" type="boolean" checked="False" label="Output final assembly graph with scaffolds?" help="Will output the final assembly graph with scaffold information in gfa format for visualisation" />
166 </inputs> 184 </inputs>
167 185
168 <outputs> 186 <outputs>
199 <assert_contents> 217 <assert_contents>
200 <has_text_matching expression="NODE_1\t1000"/> 218 <has_text_matching expression="NODE_1\t1000"/>
201 </assert_contents> 219 </assert_contents>
202 </output> 220 </output>
203 </test> 221 </test>
222 <test> <!-- Test 1 - basic test with k=33 fasta input -->
223 <param name="sc" value="false" />
224 <param name="onlyassembler" value="true"/>
225 <param name="careful" value="false" />
226 <param name="kmers" value="33" />
227 <param name="lib_type" value="paired_end" />
228 <param ftype="fasta" name="fwd_reads" value="ecoli_1K_1.fasta" />
229 <param ftype="fasta" name="rev_reads" value="ecoli_1K_2.fasta" />
230 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
231 <output name="out_contig_stats">
232 <assert_contents>
233 <has_text_matching expression="NODE_1\t1000"/>
234 </assert_contents>
235 </output>
236 </test>
237 <test> <!-- Test 1 - basic test with k=33 and gzipped input -->
238 <param name="sc" value="false" />
239 <param name="careful" value="false" />
240 <param name="kmers" value="33" />
241 <param name="lib_type" value="paired_end" />
242 <param ftype="fastq.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" />
243 <param ftype="fastq.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" />
244 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
245 <output name="out_contig_stats">
246 <assert_contents>
247 <has_text_matching expression="NODE_1\t1000"/>
248 </assert_contents>
249 </output>
250 </test>
204 <test> <!-- Test 2 - auto k --> 251 <test> <!-- Test 2 - auto k -->
205 <param name="sc" value="false" /> 252 <param name="sc" value="false" />
206 <param name="careful" value="false" /> 253 <param name="careful" value="false" />
207 <param name="auto_kmer_choice" value="true" /> 254 <param name="auto_kmer_choice" value="true" />
208 <param name="lib_type" value="paired_end" /> 255 <param name="lib_type" value="paired_end" />