Mercurial > repos > iuc > bbtools_bbmap

comparison bbmap.xml @ 9:83d0df824438 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
author iuc
date Tue, 27 Aug 2024 10:13:16 +0000
parents 3fa2af3231df
children 57136caabb32
comparison
equal deleted inserted replaced
8:33262f7b3e23 9:83d0df824438
2 <description>short-read aligner</description> 2 <description>short-read aligner</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/> 6 <expand macro="edam_ontology"/>
7 <xrefs>
8 <xref type="bio.tools">bbmap</xref>
9 </xrefs>
7 <expand macro="requirements"/> 10 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
9 #import os
10 #import re
11
12 #if str($ref_source_cond.ref_source) == 'cached' 12 #if str($ref_source_cond.ref_source) == 'cached'
13 #set ref = str($ref_source_cond.reference.fields.path) 13 #set ref = str($ref_source_cond.reference.fields.path)
14 #else: 14 #else:
15 #set ref = $ref_source_cond.reference 15 #set ref = $ref_source_cond.reference
16 #end if 16 #end if
29 #set read2_file = 'reverse' + $ext 29 #set read2_file = 'reverse' + $ext
30 ln -s '${read2}' '${read2_file}' && 30 ln -s '${read2}' '${read2_file}' &&
31 #end if 31 #end if
32 #else: 32 #else:
33 #set read1 = $input_type_cond.reads_collection['forward'] 33 #set read1 = $input_type_cond.reads_collection['forward']
34 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
35 ## bbmap uses the file extension to determine the input format. 34 ## bbmap uses the file extension to determine the input format.
36 #set ext = $read1_identifier + '.fastq' 35 #set ext = '.fastq'
37 #if $read1.ext.endswith('.gz'): 36 #if $read1.ext.endswith('.gz'):
38 #set ext = $ext + '.gz' 37 #set ext = $ext + '.gz'
39 #end if 38 #end if
40 #set read1_file = $read1_identifier + $ext 39 #set read1_file = 'forward' + $ext
41 ln -s '${read1}' '${read1_file}' && 40 ln -s '${read1}' '${read1_file}' &&
42 #set read2 = $input_type_cond.reads_collection['reverse'] 41 #set read2 = $input_type_cond.reads_collection['reverse']
43 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) 42 #set read2_file = 'reverse' + $ext
44 #set read2_file = $read2_identifier + $ext
45 ln -s '${read2}' '${read2_file}' && 43 ln -s '${read2}' '${read2_file}' &&
46 #end if 44 #end if
47 45
48 bbmap.sh 46 bbmap.sh
49 47
202 <option value="lr">Trim both</option> 200 <option value="lr">Trim both</option>
203 </param> 201 </param>
204 <param argument="untrim" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Undo trimming after mapping?" help="Untrimmed bases will be soft-clipped in cigar strings"/> 202 <param argument="untrim" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Undo trimming after mapping?" help="Untrimmed bases will be soft-clipped in cigar strings"/>
205 <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/> 203 <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
206 <param argument="mintrimlength" type="integer" value="60" label="Don't trim reads to be shorter than this value"/> 204 <param argument="mintrimlength" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
207 <param argument="fakefastaquality" type="integer" value="-1" max="50" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/> 205 <param argument="fakefastaquality" type="integer" max="50" value="-1" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/>
208 <param argument="ignorebadquality" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Keep going, rather than crashing, if a read has out-of-range quality values?"/> 206 <param argument="ignorebadquality" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Keep going, rather than crashing, if a read has out-of-range quality values?"/>
209 <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/> 207 <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
210 <param argument="minaveragequality" type="integer" value="0" label="Do not map reads with average quality below this value"/> 208 <param argument="minaveragequality" type="integer" value="0" label="Do not map reads with average quality below this value"/>
211 <param argument="maqb" type="integer" value="0" label="Calculate maq from this many initial bases" help="Zero value ignores"/> 209 <param argument="maqb" type="integer" value="0" label="Calculate maq from this many initial bases" help="Zero value ignores"/>
212 </section> 210 </section>
225 <option value="name">Sort by read names</option> 223 <option value="name">Sort by read names</option>
226 <option value="unsorted">Not sorted (sorted as input)</option> 224 <option value="unsorted">Not sorted (sorted as input)</option>
227 </param> 225 </param>
228 </section> 226 </section>
229 <section name="pf_options" title="Post-filtering options"> 227 <section name="pf_options" title="Post-filtering options">
230 <param argument="idfilter" type="integer" value="0" min="0" max="1" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/> 228 <param argument="idfilter" type="integer" min="0" max="1" value="0" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/>
231 <param argument="subfilter" type="integer" value="-1" label="Ban alignments with more than this many substitutions" help="Negative value ignores"/> 229 <param argument="subfilter" type="integer" value="-1" label="Ban alignments with more than this many substitutions" help="Negative value ignores"/>
232 <param argument="insfilter" type="integer" value="-1" label="Ban alignments with more than this many insertions" help="Negative value ignores"/> 230 <param argument="insfilter" type="integer" value="-1" label="Ban alignments with more than this many insertions" help="Negative value ignores"/>
233 <param argument="delfilter" type="integer" value="-1" label="Ban alignments with more than this many deletions" help="Negative value ignores"/> 231 <param argument="delfilter" type="integer" value="-1" label="Ban alignments with more than this many deletions" help="Negative value ignores"/>
234 <param argument="indelfilter" type="integer" value="-1" label="Ban alignments with more than this many indels" help="Negative value ignores"/> 232 <param argument="indelfilter" type="integer" value="-1" label="Ban alignments with more than this many indels" help="Negative value ignores"/>
235 <param argument="editfilter" type="integer" value="-1" label="Ban alignments with more than this many edits" help="Negative value ignores"/> 233 <param argument="editfilter" type="integer" value="-1" label="Ban alignments with more than this many edits" help="Negative value ignores"/>
365 * Not sorted (sorted as input) - the file is sorted in the order of the reads in the input file. 363 * Not sorted (sorted as input) - the file is sorted in the order of the reads in the input file.
366 364
367 </help> 365 </help>
368 <expand macro="citations"/> 366 <expand macro="citations"/>
369 </tool> 367 </tool>
370