Mercurial > repos > bgruening > canu
comparison canu.xml @ 1:58346ef3116b draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/canu commit 21c4301d86a46ba48759ffeb4a0b7f3c269558e4
author | bgruening |
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date | Sat, 09 Jun 2018 13:46:56 -0400 |
parents | 4c8f32256fa8 |
children | c5b7390290b1 |
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0:4c8f32256fa8 | 1:58346ef3116b |
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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. |