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comparison bowtie2_wrapper.xml @ 20:fcc6efc4ef6d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 1912a560c3ad87117f18570fcf3ba4af4f924340
author iuc
date Tue, 23 Jan 2018 12:20:00 -0500
parents 7f9d1892eb1b
children e798c0b3384c
comparison
equal deleted inserted replaced
19:7f9d1892eb1b 20:fcc6efc4ef6d
1 <tool id="bowtie2" name="Bowtie2" version="2.3.4" profile="17.01"> 1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.1" profile="17.01">
2 <description>- map reads against reference genome</description> 2 <description>- map reads against reference genome</description>
3 <macros> 3 <macros>
4 <import>bowtie2_macros.xml</import> 4 <import>bowtie2_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
280 #end if 280 #end if
281 281
282 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes": 282 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
283 ${analysis_type.sam_options.no_unal} 283 ${analysis_type.sam_options.no_unal}
284 ${analysis_type.sam_options.omit_sec_seq} 284 ${analysis_type.sam_options.omit_sec_seq}
285 ${analysis_type.sam_options.sam-no-qname-trunc} 285 ${analysis_type.sam_options.sam_no_qname_trunc}
286 ${analysis_type.sam_options.xeq} 286 ${analysis_type.sam_options.xeq}
287 ${analysis_type.sam_options.soft-clipped-unmapped-tlen} 287 ${analysis_type.sam_options.soft_clipped_unmapped_tlen}
288 #end if 288 #end if
289 289
290 #if str( $analysis_type.other_options.other_options_selector ) == "yes": 290 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
291 ${analysis_type.other_options.reorder} 291 ${analysis_type.other_options.reorder}
292 ${analysis_type.other_options.non_deterministic} 292 ${analysis_type.other_options.non_deterministic}
501 <option value="no" selected="true">No</option> 501 <option value="no" selected="true">No</option>
502 </param> 502 </param>
503 <when value="yes"> 503 <when value="yes">
504 <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/> 504 <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
505 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/> 505 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
506 <param argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/> 506 <param name="sam_no_qname_trunc" argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
507 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/> 507 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
508 <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/> 508 <param name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
509 </when> 509 </when>
510 <when value="no"> 510 <when value="no">
511 <!-- do nothing --> 511 <!-- do nothing -->
512 </when> 512 </when>
513 </conditional> 513 </conditional>