Mercurial > repos > iuc > minimap2
comparison minimap2.xml @ 4:6f50f36e4481 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit 2d2b68971e74ecb099e2c1109f7176d7fcbf8ec7
author | iuc |
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date | Tue, 07 Aug 2018 07:59:53 -0400 |
parents | 1650a97189be |
children | 17e61517c166 |
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3:1650a97189be | 4:6f50f36e4481 |
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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 |