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comparison minimap2.xml @ 11:5c73cef26bbe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
author iuc
date Tue, 07 Aug 2018 07:59:27 -0400
parents 8cc404188fae
children 440100db1333
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10:8cc404188fae 11:5c73cef26bbe
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="minimap2" name="Map with minimap2" version="2.5" profile="17.01"> 2 <tool id="minimap2" name="Map with minimap2" version="2.5+gx1" profile="17.01">
3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description> 3 <description>A fast pairwise aligner for genomic and spliced nucleotide sequences</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.5">minimap2</requirement> 5 <requirement type="package" version="2.5">minimap2</requirement>
6 <requirement type="package" version="1.6">samtools</requirement> 6 <requirement type="package" version="1.6">samtools</requirement>
7 </requirements> 7 </requirements>
11 #if $reference_source.reference_source_selector == 'history': 11 #if $reference_source.reference_source_selector == 'history':
12 ln -f -s '$reference_source.ref_file' reference.fa && 12 ln -f -s '$reference_source.ref_file' reference.fa &&
13 #else: 13 #else:
14 ln -f -s '$reference_source.ref_file.fields.path' reference.fa && 14 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
15 #end if 15 #end if
16 minimap2 -a 16 minimap2
17 -x $analysis_type_selector 17 -x $analysis_type_selector
18 ## indexing options 18 ## indexing options
19 #if $indexing_options.k: 19 #if $indexing_options.k:
20 -k $indexing_options.k 20 -k $indexing_options.k
21 #end if 21 #end if
98 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']: 98 #if $fastq_input.fastq_input_selector in ['single', 'paired_iv']:
99 '$fastq_input.fastq_input1' 99 '$fastq_input.fastq_input1'
100 #else if $fastq_input.fastq_input_selector == 'paired': 100 #else if $fastq_input.fastq_input_selector == 'paired':
101 '$fastq_input.fastq_input1' '$fastq_input.fastq_input2' 101 '$fastq_input.fastq_input1' '$fastq_input.fastq_input2'
102 #else if $fastq_input.fastq_input_selector == 'paired_collection': 102 #else if $fastq_input.fastq_input_selector == 'paired_collection':
103 '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse' 103 '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
104 #end if 104 #end if
105 | samtools sort 105 #if $io_options.output_format == 'BAM':
106 -@\${GALAXY_SLOTS:-2} 106 -a
107 -O $io_options.output_format 107 | samtools sort
108 #if $io_options.output_format == 'CRAM': 108 -@\${GALAXY_SLOTS:-2}
109 -O $io_options.output_format
110 -o '$alignment_output'
111 #else if $io_options.output_format == 'CRAM':
112 -a
113 | samtools sort
114 -@\${GALAXY_SLOTS:-2}
115 -O $io_options.output_format
109 --reference reference.fa 116 --reference reference.fa
110 --output-fmt-option no_ref 117 --output-fmt-option no_ref
111 #end if 118 -o '$alignment_output'
112 -o '$alignment_output' 119 #end if
120 > '$alignment_output'
113 ]]> 121 ]]>
114 </command> 122 </command>
115 <inputs> 123 <inputs>
116 <conditional name="reference_source"> 124 <conditional name="reference_source">
117 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> 125 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
118 <option value="cached">Use a built-in genome index</option> 126 <option value="cached">Use a built-in genome index</option>
119 <option value="history">Use a genome from history and build index</option> 127 <option value="history">Use a genome from history and build index</option>
120 </param> 128 </param>
121 <when value="cached"> 129 <when value="cached">
122 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> 130 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
126 </options> 134 </options>
127 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 135 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
128 </param> 136 </param>
129 </when> 137 </when>
130 <when value="history"> 138 <when value="history">
131 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" /> 139 <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
132 </when> 140 </when>
133 </conditional> 141 </conditional>
134 <section name="indexing_options" title="Indexing options"> 142 <section name="indexing_options" title="Indexing options">
135 <!-- Homopolymer setting seems to not properly overwrite sr preset 143 <!-- Homopolymer setting seems to not properly overwrite sr preset
136 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/> 144 <param argument="-H" name="H" type="boolean" optional="true" truevalue="-H" falsevalue="" label="Use homopolymer-compressed k-mer ?"/>
198 <option value="f">transcript strand</option> 206 <option value="f">transcript strand</option>
199 <option value="b">both strands</option> 207 <option value="b">both strands</option>
200 </param> 208 </param>
201 </section> 209 </section>
202 <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False"> 210 <section name="io_options" title="Set advanced output options" help="Sets -Q, -L, -R, -c, --cs and -K options." expanded="False">
203 <param name="output_format" type="select" label="Produce BAM or CRAM file?"> 211 <param name="output_format" type="select" label="Select an output format">
204 <option value="BAM">BAM</option> 212 <option value="BAM">BAM</option>
205 <option value="CRAM">CRAM</option> 213 <option value="CRAM">CRAM</option>
214 <option value="paf">paf</option>
206 </param> 215 </param>
207 <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" optional="true" label="don't output base quality"/> 216 <param argument="-Q" type="boolean" truevalue="-Q" falsevalue="" optional="true" label="don't output base quality"/>
208 <param argument="-L" type="boolean" truevalue="-L" falsevalue="" optional="true" label="write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/> 217 <param argument="-L" type="boolean" truevalue="-L" falsevalue="" optional="true" label="write CIGAR with >65535 ops to the CG tag" help="Useful for very long reads in SAM/BAM format"/>
209 <param argument="-K" type="integer" optional="true" label="minibatch size for mapping (in megabyte)" help="default=500M"/> 218 <param argument="-K" type="integer" optional="true" label="minibatch size for mapping (in megabyte)" help="default=500M"/>
210 <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below."> 219 <param argument="--cs" type="select" optional="true" label="Output cs tag?" help="The cs tag is a more compact standalone representation of the MD tag, see help below.">
233 </action> 242 </action>
234 </when> 243 </when>
235 </conditional> 244 </conditional>
236 </actions> 245 </actions>
237 <change_format> 246 <change_format>
247 <when input="io_options.output_format" value="paf" format="tabular" />
238 <when input="io_options.output_format" value="CRAM" format="cram" /> 248 <when input="io_options.output_format" value="CRAM" format="cram" />
239 </change_format> 249 </change_format>
240 </data> 250 </data>
241 </outputs> 251 </outputs>
242 <tests> 252 <tests>
299 <param name="ref_file" value="bwa-mem-mt-genome"/> 309 <param name="ref_file" value="bwa-mem-mt-genome"/>
300 <param name="fastq_input_selector" value="single"/> 310 <param name="fastq_input_selector" value="single"/>
301 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> 311 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
302 <param name="analysis_type_selector" value="sr"/> 312 <param name="analysis_type_selector" value="sr"/>
303 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" /> 313 <output name="alignment_output" ftype="bam" file="minimap2-test1-fasta.bam" lines_diff="2" />
314 </test>
315 <test>
316 <!-- test paf output -->
317 <param name="reference_source_selector" value="history" />
318 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" />
319 <param name="fastq_input_selector" value="single"/>
320 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" />
321 <param name="analysis_type_selector" value="ava-ont"/>
322 <param name="output_format" value="paf"/>
323 <output name="alignment_output" ftype="tabular" file="mini_reads.paf" />
304 </test> 324 </test>
305 </tests> 325 </tests>
306 <help> 326 <help>
307 327
308 Users’ Guide 328 Users’ Guide