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comparison pilon.xml @ 1:11e5408fd238 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit f11cbbf24637c96c53e4a1ea5ace4b21e116677c
author iuc
date Tue, 04 Apr 2017 11:18:37 -0400
parents fe0dc27e6327
children
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0:fe0dc27e6327 1:11e5408fd238
1 <tool id="pilon" name="pilon" version="0.1"> 1 <tool id="pilon" name="pilon" version="1.20.1">
2 <description>An automated genome assembly improvement and variant detection tool</description> 2 <description>An automated genome assembly improvement and variant detection tool</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.18">pilon</requirement> 4 <requirement type="package" version="1.20">pilon</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #if $auto_selection.auto_enabled == "yes" 7 #if $auto_selection.auto_enabled == "yes"
8 #for $bamfile in $auto_selection.bam 8 #for $bamfile in $auto_selection.bam
9 ln -f -s "$bamfile" "\$(basename $bamfile)" && 9 ln -f -s "$bamfile" "\$(basename $bamfile)" &&
68 --chunksize $options.chunk_size 68 --chunksize $options.chunk_size
69 $options.diploid 69 $options.diploid
70 $options.duplicates 70 $options.duplicates
71 $options.iupac 71 $options.iupac
72 $options.nonpf 72 $options.nonpf
73 #if len($options.targetlist.strip()) > 0 73 #if len($options.targets.strip()) > 0
74 --targetlist $options.targetlist 74 --targets $options.targets
75 #end if 75 #end if
76 --fix $options.fixes 76 --fix $options.fixes
77 $options.verbose 77 $options.verbose
78 --defaultqual $options.defaultqual 78 --defaultqual $options.defaultqual
79 --flank $options.flank 79 --flank $options.flank
93 <param label="Source for reference genome used for BAM alignments" name="reference_genome_source" type="select"> 93 <param label="Source for reference genome used for BAM alignments" name="reference_genome_source" type="select">
94 <option selected="True" value="history">Use a genome from history</option> 94 <option selected="True" value="history">Use a genome from history</option>
95 <option value="builtin">Use a built-in genome"</option> 95 <option value="builtin">Use a built-in genome"</option>
96 </param> 96 </param>
97 <when value="history"> 97 <when value="history">
98 <param format="fasta" type="data" metadata_name="dbkey" name="history_item" /> 98 <param format="fasta" type="data" name="history_item" label="Select a reference genome"/>
99 </when> 99 </when>
100 <when value="builtin"> 100 <when value="builtin">
101 <param label="Select a reference genome" name="builtin" type="select"> 101 <param label="Select a reference genome" name="builtin" type="select">
102 <options from_data_table="all_fasta"> 102 <options from_data_table="all_fasta">
103 <filter column="2" type="sort_by" /> 103 <filter column="2" type="sort_by" />
166 <option value="local">Detect and fix local misassemblies</option> 166 <option value="local">Detect and fix local misassemblies</option>
167 <option value="none">Do none of these fixes (no FASTA will be written)</option> 167 <option value="none">Do none of these fixes (no FASTA will be written)</option>
168 <option value="amb">Fix ambigious bases in FASTA output (experimental)</option> 168 <option value="amb">Fix ambigious bases in FASTA output (experimental)</option>
169 <option value="breaks">Allow local reassembly to open new gaps (experimental, requires local assembly fixing to be selected)</option> 169 <option value="breaks">Allow local reassembly to open new gaps (experimental, requires local assembly fixing to be selected)</option>
170 <option value="novel">Assemble novel sequence from unaligned non-jump reads (experimental)</option> 170 <option value="novel">Assemble novel sequence from unaligned non-jump reads (experimental)</option>
171 <!-- TODO: enable this when documented in pilon <option value="circle">Trim long reads for circular continuity(experimental, requires unpaired reads)</option>-->
171 </param> 172 </param>
172 <param argument="diploid" label="Organism is diploid" type="boolean" checked="false" 173 <param argument="diploid" label="Organism is diploid" type="boolean" checked="false"
173 help="Sample is from diploid organism; will eventually affect calling of heterozygous SNPs" 174 help="Sample is from diploid organism; will eventually affect calling of heterozygous SNPs"
174 truevalue="--diploid" falsevalue="" /> 175 truevalue="--diploid" falsevalue="" />
175 <param argument="duplicates" label="Use duplicates" type="boolean" checked="false" 176 <param argument="duplicates" label="Use duplicates" type="boolean" checked="false"
179 help="Output IUPAC ambiguous base codes in the output FASTA file when appropriate" 180 help="Output IUPAC ambiguous base codes in the output FASTA file when appropriate"
180 truevalue="--iupac" falsevalue="" /> 181 truevalue="--iupac" falsevalue="" />
181 <param argument="nonpf" label="Use low quality reads" type="boolean" checked="false" 182 <param argument="nonpf" label="Use low quality reads" type="boolean" checked="false"
182 help="Use reads which failed sequencer quality filtering" 183 help="Use reads which failed sequencer quality filtering"
183 truevalue="--nonpf" falsevalue="" /> 184 truevalue="--nonpf" falsevalue="" />
184 <param argument="targetlist" label="List of targets to process (leave blank for all)" default="" type="text" length="40" 185 <param argument="targets" label="List of targets to process (leave blank for all)" type="text"
185 help="Only process the specified target(s). Targets are comma-separated, and each target is a fasta element name optionally followed by a base range." /> 186 help="Only process the specified target(s). Targets are comma-separated, and each target is a fasta element name optionally followed by a base range." />
186 <param argument="verbose" label="Verbose output (in tool log)" type="boolean" check="false" 187 <param argument="verbose" label="Verbose output (in tool log)" type="boolean" checked="false"
187 truevalue="--verbose" falsevalue="" /> 188 truevalue="--verbose" falsevalue="" />
188 <param argument="defaultqual" label="Default base quality" type="integer" min="1" value="15" 189 <param argument="defaultqual" label="Default base quality" type="integer" min="1" value="15"
189 help="Assumes bases are of this quality if quals are no present in input BAMs" /> 190 help="Assumes bases are of this quality if quals are no present in input BAMs" />
190 <param argument="flank" label="Flanking bases to ignore" type="integer" min="1" value="10" 191 <param argument="flank" label="Flanking bases to ignore" type="integer" min="1" value="10"
191 help="This many bases at each end of the good reads will be ignored." /> 192 help="This many bases at each end of the good reads will be ignored." />