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comparison spades.xml @ 6:65c2d63fcbe6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340
author iuc
date Sat, 13 May 2017 15:51:58 -0400
parents 909c315b656d
children 9006e5836729
comparison
equal deleted inserted replaced
5:909c315b656d 6:65c2d63fcbe6
68 #for $contig in $untrusted_contigs: 68 #for $contig in $untrusted_contigs:
69 #if $contig: 69 #if $contig:
70 --untrusted-contigs $contig.extension:$contig 70 --untrusted-contigs $contig.extension:$contig
71 #end if 71 #end if
72 #end for 72 #end for
73 && cat contigs.fasta | python '$write_tsv_script' > '$out_contig_stats'
74 && cat scaffolds.fasta | python '$write_tsv_script' > '$out_scaffold_stats'
73 ]]> 75 ]]>
74 </command> 76 </command>
75 <inputs> 77 <inputs>
76 <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean"> 78 <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean">
77 <option value="false">No</option> 79 <option value="false">No</option>
139 <param optional="true" format="fastq" label="Nanopore reads" multiple="true" name="nanopore_reads" type="data" /> 141 <param optional="true" format="fastq" label="Nanopore reads" multiple="true" name="nanopore_reads" type="data" />
140 <param optional="true" format="fasta,fastq" label="Sanger reads" multiple="true" name="sanger_reads" type="data" /> 142 <param optional="true" format="fasta,fastq" label="Sanger reads" multiple="true" name="sanger_reads" type="data" />
141 <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" /> 143 <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
142 <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" /> 144 <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
143 </inputs> 145 </inputs>
146 <configfiles>
147 <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python
148 import sys,re
149 search_str = r'^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$'
150 replace_str = r'\1_\2\t\3\t\4'
151 cmd = re.compile(search_str)
152 sys.stdout.write('#name\tlength\tcoverage\n')
153 for i,line in enumerate(sys.stdin):
154 if cmd.match(line):
155 sys.stdout.write(cmd.sub(replace_str,line))
156 ]]>
157 </configfile>
158 </configfiles>
159
144 <outputs> 160 <outputs>
161 <data format="tabular" label="SPAdes contig stats" name="out_contig_stats" >
162 <actions>
163 <action name="column_names" type="metadata" default="name,length,coverage"/>
164 </actions>
165 </data>
166 <data format="tabular" label="SPAdes scaffold stats" name="out_scaffold_stats" >
167 <actions>
168 <action name="column_names" type="metadata" default="name,length,coverage"/>
169 </actions>
170 </data>
145 <data format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" name="out_contigs" /> 171 <data format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" name="out_contigs" />
146 <data format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" name="out_scaffolds" /> 172 <data format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" name="out_scaffolds" />
147 <data format="txt" from_work_dir="spades.log" label="SPAdes log" name="out_log" /> 173 <data format="txt" from_work_dir="spades.log" label="SPAdes log" name="out_log" />
148 </outputs> 174 </outputs>
149 <tests> 175 <tests>
153 <param name="kmers" value="33" /> 179 <param name="kmers" value="33" />
154 <param name="lib_type" value="paired_end" /> 180 <param name="lib_type" value="paired_end" />
155 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> 181 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
156 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" /> 182 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
157 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> 183 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
184 <output name="out_contig_stats">
185 <assert_contents>
186 <has_text_matching expression="NODE_1\t1000\t225"/>
187 </assert_contents>
188 </output>
158 </test> 189 </test>
159 <test> 190 <test>
160 <param name="sc" value="false" /> 191 <param name="sc" value="false" />
161 <param name="careful" value="false" /> 192 <param name="careful" value="false" />
162 <param name="auto_kmer_choice" value="true" /> 193 <param name="auto_kmer_choice" value="true" />