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comparison canu.xml @ 1:58346ef3116b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
author bgruening
date Sat, 09 Jun 2018 13:46:56 -0400
parents 4c8f32256fa8
children c5b7390290b1
comparison
equal deleted inserted replaced
0:4c8f32256fa8 1:58346ef3116b
13 cp '$input' ./input_${counter}.gz && 13 cp '$input' ./input_${counter}.gz &&
14 #end if 14 #end if
15 #end for 15 #end for
16 16
17 canu 17 canu
18 $stage 18 #if $stage != 'all':
19 $stage
20 #end if
19 -p canu 21 -p canu
20 -d out_dir 22 -d out_dir
21 #if $s: 23 #if $s:
22 -s '$s' 24 -s '$s'
23 #end if 25 #end if
61 #else: 63 #else:
62 '$input' 64 '$input'
63 #end if 65 #end if
64 #end for 66 #end for
65 2>&1 67 2>&1
68 &&
69 echo "Check echo"
66 ]]> 70 ]]>
67 </command> 71 </command>
68 <inputs> 72 <inputs>
69 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="Input reads" /> 73 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="Input reads" />
70 <param name="mode" type="select" label="Mode"> 74 <param name="mode" type="select" label="Mode">
72 <option value="-nanopore-corrected">Nanopore corrected</option> 76 <option value="-nanopore-corrected">Nanopore corrected</option>
73 <option value="-pacbio-raw">PacBio raw</option> 77 <option value="-pacbio-raw">PacBio raw</option>
74 <option value="-pacbio-corrected">PacBio corrected</option> 78 <option value="-pacbio-corrected">PacBio corrected</option>
75 </param> 79 </param>
76 <param name="stage" type="select" label="To restrict canu to only a specific stage, use"> 80 <param name="stage" type="select" label="To restrict canu to only a specific stage, use">
77 <option value="" selected="true">all</option> 81 <option value="all" selected="true">all</option>
78 <option value="-correct">generate corrected reads</option> 82 <option value="-correct">generate corrected reads</option>
79 <option value="-trim">generate trimmed reads</option> 83 <option value="-trim">generate trimmed reads</option>
80 <option value="-assemble">generate an assembly</option> 84 <option value="-assemble">generate an assembly</option>
81 <option value="-trim-assemble">generate trimmed reads and then assemble them</option> 85 <option value="-trim-assemble">generate trimmed reads and then assemble them</option>
82 </param> 86 </param>
83 <param argument="genomeSize" type="text" label="Estimated genome size (e.g. 80m, 15k, 2g)" /> 87 <param argument="genomeSize" type="text" label="Estimated genome size (e.g. 80m, 15k, 2g)">
88 <validator type="empty_field" />
89 </param>
84 <param argument="rawErrorRate" type="float" value="" optional="true" min="0" max="1" 90 <param argument="rawErrorRate" type="float" value="" optional="true" min="0" max="1"
85 label="Maximum raw overlap mismatch" help="The defaults are 0.300 for PacBio reads and 0.500 for Nanopore reads." /> 91 label="Maximum raw overlap mismatch" help="The defaults are 0.300 for PacBio reads and 0.500 for Nanopore reads." />
86 <param argument="correctedErrorRate" type="float" value="" optional="true" min="0" max="1" 92 <param argument="correctedErrorRate" type="float" value="" optional="true" min="0" max="1"
87 label="Maximum corrected overlap mismatch" help="The allowed difference in an overlap between two corrected reads. Assemblies of 93 label="Maximum corrected overlap mismatch" help="The allowed difference in an overlap between two corrected reads. Assemblies of
88 low coverage or data with biological differences will benefit from a slight increase 94 low coverage or data with biological differences will benefit from a slight increase
100 <param argument="lowCovDepth" type="integer" value="5" min="0" label="Low coverage depth" /> 106 <param argument="lowCovDepth" type="integer" value="5" min="0" label="Low coverage depth" />
101 </section> 107 </section>
102 </inputs> 108 </inputs>
103 <outputs> 109 <outputs>
104 <data name="contigs" format="fasta" from_work_dir="out_dir/canu.contigs.fasta" label="${tool.name} on ${on_string} (contigs)"> 110 <data name="contigs" format="fasta" from_work_dir="out_dir/canu.contigs.fasta" label="${tool.name} on ${on_string} (contigs)">
111 <filter>stage == 'all'</filter>
105 </data> 112 </data>
106 <data name="unassembled" format="fasta" from_work_dir="out_dir/canu.unassembled.fasta" label="${tool.name} on ${on_string} (contigs)"> 113 <data name="unassembled" format="fasta" from_work_dir="out_dir/canu.unassembled.fasta" label="${tool.name} on ${on_string} (unassembled)">
114 <filter>stage == 'all'</filter>
107 </data> 115 </data>
108 <data name="unitigs" format="fasta" from_work_dir="out_dir/canu.unitigs.fasta" label="${tool.name} on ${on_string} (unitigs)"> 116 <data name="unitigs" format="fasta" from_work_dir="out_dir/canu.unitigs.fasta" label="${tool.name} on ${on_string} (unitigs)">
117 <filter>stage == 'all'</filter>
109 </data> 118 </data>
110 <data name="corrected_reads" format="fasta.gz" from_work_dir="out_dir/canu.correctedReads.fasta.gz" label="${tool.name} on ${on_string} (unitigs)"> 119 <data name="corrected_reads" format="fasta.gz" from_work_dir="out_dir/canu.correctedReads.fasta.gz" label="${tool.name} on ${on_string} (corrected reads)">
120 <filter>'-correct' in stage or stage == 'all'</filter>
121 </data>
122 <data name="trimmed_reads" format="fasta.gz" from_work_dir="out_dir/canu.trimmedReads.fasta.gz" label="${tool.name} on ${on_string} (trimmed reads)">
123 <filter>'-trim' in stage or stage == 'all'</filter>
111 </data> 124 </data>
112 </outputs> 125 </outputs>
113 <tests> 126 <tests>
114 <test> 127 <test expect_num_outputs="5">
115 <!-- test multiple input -->
116 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/> 128 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/>
117 <param name="genomeSize" value="4.6m" /> 129 <param name="genomeSize" value="4.6m" />
118 <param name="minReadLength" value="2000" /> 130 <param name="minReadLength" value="2000" />
119 <output name="contigs" ftype="fasta" file="ecoli_canu_contigs.fa"/> 131 <output name="contigs" ftype="fasta" file="ecoli_canu_contigs_result1.fa"/>
120 <output name="unitigs" ftype="fasta" file="ecoli_canu_unitigs.fa"/> 132 <output name="unitigs" ftype="fasta" file="ecoli_canu_unitigs_result1.fa"/>
121 <output name="unassembled" ftype="fasta" file="ecoli_unassembled.fa"/> 133 <output name="unassembled" ftype="fasta" file="ecoli_canu_unassembled_result1.fa"/>
134 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result1.fa.gz"/>
135 <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result1.fa.gz"/>
122 </test> 136 </test>
123 137 <test expect_num_outputs="5">
124 <test >
125 <!-- test multiple input -->
126 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/> 138 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/>
127 <param name="genomeSize" value="4.6m" /> 139 <param name="genomeSize" value="4.6m" />
128 <param name="minReadLength" value="2000" /> 140 <param name="minReadLength" value="2000" />
129 <param name="minOverlapLength" value="800" /> 141 <param name="minOverlapLength" value="800" />
130 <param name="rawErrorRate" value="0.2" /> 142 <param name="rawErrorRate" value="0.2" />
131 <param name="correctedErrorRate" value="0.05" /> 143 <param name="correctedErrorRate" value="0.05" />
132 <param name="corOutCoverage" value="2" /> 144 <param name="corOutCoverage" value="2" />
133 <output name="contigs" ftype="fasta" file="canu_contigs_result1.fa"/> 145 <output name="contigs" ftype="fasta" file="ecoli_canu_contigs_result2.fa"/>
134 <output name="unitigs" ftype="fasta" file="canu_unitigs_result1.fa"/> 146 <output name="unitigs" ftype="fasta" file="ecoli_canu_unitigs_result2.fa"/>
135 <output name="unassembled" ftype="fasta" file="canu_unassembled_result1.fa"/> 147 <output name="unassembled" ftype="fasta" file="ecoli_canu_unassembled_result2.fa"/>
148 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result2.fa.gz"/>
149 <output name="trimmed_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_trimmed_reads_result2.fa.gz"/>
136 </test> 150 </test>
137 <test> 151 <test expect_num_outputs="1">
138 <!-- test multiple input -->
139 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/> 152 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/>
140 <param name="minReadLength" value="2000" />
141 <param name="stage" value="-correct"/> 153 <param name="stage" value="-correct"/>
154 <param name="minReadLength" value="2500" />
142 <param name="genomeSize" value="4.6m" /> 155 <param name="genomeSize" value="4.6m" />
143 <section name="contigFilter"> 156 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="ecoli_canu_corrected_reads_result3.fa.gz"/>
144 <param name="minReads" value="10" /> 157 </test>
145 </section> 158 <test expect_num_outputs="1">
146 <output name="corrected_reads" ftype="fasta.gz" decompress="True" file="canu_corrected_reads.fa.gz"/> 159 <param name="inputs" ftype="fasta" value="ecoli-reads.fasta"/>
147 </test> 160 <param name="stage" value="-trim"/>
161 <param name="minReadLength" value="2500" />
162 <param name="genomeSize" value="4.6m" />
163 <output name="trimmed_reads" ftype="fasta.gz" compare="sim_size" delta="12000" file="ecoli_canu_trimmed_reads_result4.fa.gz"/>
164 </test>
148 </tests> 165 </tests>
149 <help> 166 <help>
150 <![CDATA[ 167 <![CDATA[
151 168
152 Canu specializes in assembling PacBio or Oxford Nanopore sequences. Canu operates in three phases: correction, trimming and assembly. 169 Canu specializes in assembling PacBio or Oxford Nanopore sequences. Canu operates in three phases: correction, trimming and assembly.