Mercurial > repos > bgruening > nanopolish_variants

comparison nanopolish_variants.xml @ 1:1ebed8b65752 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9
author bgruening
date Tue, 05 Jun 2018 17:58:46 -0400
parents 639b3a5bb415
children bc79b5b0fe04
comparison
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0:639b3a5bb415 1:1ebed8b65752
15 #end if 15 #end if
16 16
17 nanopolish index -d fast5_files/ reads.fasta && 17 nanopolish index -d fast5_files/ reads.fasta &&
18 ln -s '$b' reads.bam && 18 ln -s '$b' reads.bam &&
19 ln -s '${b.metadata.bam_index}' reads.bam.bai && 19 ln -s '${b.metadata.bam_index}' reads.bam.bai &&
20 ln -s '$g' genome.fa && 20 #if $reference_source.reference_source_selector == 'history':
21 ln -f -s '$reference_source.ref_file' genome.fa &&
22 #else:
23 ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
24 #end if
21 25
22 nanopolish variants 26 nanopolish variants
23 -r reads.fasta 27 -r reads.fasta
24 -b reads.bam 28 -b reads.bam
25 -g genome.fa 29 -g genome.fa
36 40
37 -m $min_candidate_frequency 41 -m $min_candidate_frequency
38 -d $min_candidate_depth 42 -d $min_candidate_depth
39 -x $max_haplotypes 43 -x $max_haplotypes
40 --max-rounds $max_rounds 44 --max-rounds $max_rounds
45 --threads "\${GALAXY_SLOTS:-4}"
46 #if str($min_flanking_sequence):
47 --min-flanking-sequence $min_flanking_sequence
48 #end if
41 #if $ploidy != -1: 49 #if $ploidy != -1:
42 --ploidy $ploidy 50 --ploidy $ploidy
43 #end if 51 #end if
44 52
45 #if $w and str($w).strip(): 53 #if $w and str($w).strip():
62 -a '$adv.input_alt_bc_bam' 70 -a '$adv.input_alt_bc_bam'
63 #end if 71 #end if
64 #if $adv.input_models_fofn: 72 #if $adv.input_models_fofn:
65 --models-fofn '$input_models_fofn' 73 --models-fofn '$input_models_fofn'
66 #end if 74 #end if
67
68
69 75
70 ]]></command> 76 ]]></command>
71 <inputs> 77 <inputs>
72 <!-- index inputs --> 78 <!-- index inputs -->
73 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> 79 <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
74 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/> 80 <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/>
75 81
76 <!-- variants consensus inputs --> 82 <!-- variants consensus inputs -->
77 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> 83 <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
78 <param type="data" argument="-g" format="fasta" label="The reference genome"/> 84 <conditional name="reference_source">
85 <param name="reference_source_selector" type="select" label="Load reference genome from">
86 <option value="cached">Local cache</option>
87 <option value="history">History</option>
88 </param>
89 <when value="cached">
90 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
91 <options from_data_table="all_fasta">
92 </options>
93 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
94 </param>
95 </when>
96 <when value="history">
97 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
98 </when>
99 </conditional>
79 100
80 <section name="adv" title="Optional data inputs"> 101 <section name="adv" title="Optional data inputs">
81 <!-- optional inputs --> 102 <!-- optional inputs -->
82 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/> 103 <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/>
83 <param type="data" name="input_events_bam" format="bam" optional="true" label="Events aligned to the reference genome" help="(-e)" /> 104 <param type="data" name="input_events_bam" format="bam" optional="true" label="Events aligned to the reference genome" help="(-e)" />
96 <param name="min_candidate_frequency" type="float" optional="true" value="0.2" label="Extarct if the variant frequency is at least F" help="(-m)"/> 117 <param name="min_candidate_frequency" type="float" optional="true" value="0.2" label="Extarct if the variant frequency is at least F" help="(-m)"/>
97 <param name="min_candidate_depth" type="integer" optional="true" value="20" label="Extarct if the depth is at least D" help="(-d)"/> 118 <param name="min_candidate_depth" type="integer" optional="true" value="20" label="Extarct if the depth is at least D" help="(-d)"/>
98 <param name="max_haplotypes" type="integer" optional="true" value="1000" label="Consider at most N haplotype combinations" help="(-x)"/> 119 <param name="max_haplotypes" type="integer" optional="true" value="1000" label="Consider at most N haplotype combinations" help="(-x)"/>
99 <param name="max_rounds" type="integer" optional="true" value="50" label="Perform N rounds of consensus sequence improvement" help="(--max_rounds)"/> 120 <param name="max_rounds" type="integer" optional="true" value="50" label="Perform N rounds of consensus sequence improvement" help="(--max_rounds)"/>
100 <param name="ploidy" type="integer" optional="true" value="-1" label="The ploidy level of the sequenced genome. -1:disabled" help="(-p)"/> 121 <param name="ploidy" type="integer" optional="true" value="-1" label="The ploidy level of the sequenced genome. -1:disabled" help="(-p)"/>
122 <param name="min_flanking_sequence" type="integer" optional="true" value="" label="Distance from alignment end to calculate variants" help="(--min-flanking-sequence)"/>
101 123
102 <!-- optional flags --> 124 <!-- optional flags -->
103 <param argument="--consensus" type="boolean" truevalue="--consensus" falsevalue="" checked="true" label="Consensus calling mode and output polished sequence" /> 125 <param argument="--consensus" type="boolean" truevalue="--consensus" falsevalue="" checked="true" label="Consensus calling mode and output polished sequence" />
104 <param argument="--snps" type="boolean" truevalue="--snps" falsevalue="" checked="false" label="only call SNPs"/> 126 <param argument="--snps" type="boolean" truevalue="--snps" falsevalue="" checked="false" label="only call SNPs"/>
105 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="verbose output"/> 127 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="verbose output"/>
115 <data name="output_polished" format="fasta" from_work_dir="polished.fa" label="polished sequence by consensus calling mode" /> 137 <data name="output_polished" format="fasta" from_work_dir="polished.fa" label="polished sequence by consensus calling mode" />
116 <data name="output_variants" format="vcf" from_work_dir="variants.vcf" label="Computed variants"/> 138 <data name="output_variants" format="vcf" from_work_dir="variants.vcf" label="Computed variants"/>
117 </outputs> 139 </outputs>
118 <tests> 140 <tests>
119 <test> 141 <test>
120 <!-- index test -->
121 <param name="input_merged" ftype="fasta" value="reads.fasta" /> 142 <param name="input_merged" ftype="fasta" value="reads.fasta" />
122 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> 143 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
123
124 <!-- variants consensus test -->
125 <param name="b" value="reads.sorted.bam" /> 144 <param name="b" value="reads.sorted.bam" />
126 <param name="g" value="draft.fa" /> 145 <param name="reference_source_selector" value="history" />
146 <param name="ref_file" value="draft.fa" />
127 <param name="w" value="tig00000001:200000-202000" /> 147 <param name="w" value="tig00000001:200000-202000" />
128
129 <output name="output_polished" file="polished.fa" /> 148 <output name="output_polished" file="polished.fa" />
130 <output name="output_variants" file="variants.vcf"/> 149 <output name="output_variants" file="variants.vcf"/>
131 </test> 150 </test>
132 <test> 151 <test>
133 <!-- index test -->
134 <param name="input_merged" ftype="fasta" value="reads.fasta" /> 152 <param name="input_merged" ftype="fasta" value="reads.fasta" />
135 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> 153 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
136
137 <!-- variants consensus test -->
138 <param name="b" value="reads.sorted.bam" /> 154 <param name="b" value="reads.sorted.bam" />
139 <param name="g" value="draft.fa" /> 155 <param name="reference_source_selector" value="history" />
156 <param name="ref_file" value="draft.fa" />
140 <param name="w" value="tig00000001:200000-202000" /> 157 <param name="w" value="tig00000001:200000-202000" />
141 <param name="ploidy" value="2" /> 158 <param name="ploidy" value="2" />
142 <param name="snps" value="true" /> 159 <param name="snps" value="true" />
143 <param name="faster" value="true" /> 160 <param name="faster" value="true" />
144 <param name="all_bases" value="true" /> 161 <param name="all_bases" value="true" />
145 <param name="consensus" value="false" /> 162 <param name="consensus" value="false" />
163 <param name="min_flanking_sequence" value="30" />
146 <output name="output_polished" file="t2-polished.fa" /> 164 <output name="output_polished" file="t2-polished.fa" />
147 <output name="output_variants" file="t2-variants.vcf"/> 165 <output name="output_variants" file="t2-variants.vcf"/>
148 </test> 166 </test>
149 167 <test>
168 <param name="input_merged" ftype="fasta" value="reads.fasta" />
169 <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
170 <param name="b" value="reads.sorted.bam" />
171 <param name="reference_source_selector" value="cached" />
172 <param name="ref_file" value="draft"/>
173 <param name="w" value="tig00000001:200000-202000" />
174 <output name="output_polished" file="polished.fa" />
175 <output name="output_variants" file="variants.vcf"/>
176 </test>
150 </tests> 177 </tests>
151 <help><![CDATA[ 178 <help><![CDATA[
152 179
153 Build an index mapping from basecalled reads to the signals measured by the sequencer 180 Build an index mapping from basecalled reads to the signals measured by the sequencer
154 and 181 and