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comparison bowtie2_wrapper.xml @ 25:749c918495f7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit be3590f33762e4797eaa1462d495e8e8a1b98110"
author iuc
date Fri, 23 Aug 2019 13:24:25 -0400
parents 017aba02828d
children 09b2cdb7ace5
comparison
equal deleted inserted replaced
24:017aba02828d 25:749c918495f7
1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.3" profile="18.01"> 1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.3+galaxy0" profile="18.01">
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>
279 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes": 279 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
280 -D ${analysis_type.effort_options.D} 280 -D ${analysis_type.effort_options.D}
281 -R ${analysis_type.effort_options.R} 281 -R ${analysis_type.effort_options.R}
282 #end if 282 #end if
283 #if str( $analysis_type.other_options.other_options_selector ) == "yes": 283 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
284 ${analysis_type.other_options.reorder}
285 ${analysis_type.other_options.non_deterministic} 284 ${analysis_type.other_options.non_deterministic}
286 --seed ${analysis_type.other_options.seed} 285 --seed ${analysis_type.other_options.seed}
287 #end if 286 #end if
288 287
289 #elif str( $analysis_type.analysis_type_selector ) == "cline": 288 #elif str( $analysis_type.analysis_type_selector ) == "cline":
312 #else: 311 #else:
313 > '$output' 312 > '$output'
314 #end if 313 #end if
315 314
316 ## rename unaligned sequence files 315 ## rename unaligned sequence files
317 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: 316 #if ($library.type == "paired" or $library.type == "paired_collection") and $output_unaligned_reads_l and $output_unaligned_reads_r:
318 #from os.path import splitext 317 #from os.path import splitext
319 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) ) 318 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
320 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l' 319 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
321 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r' 320 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
322 #end if 321 #end if
323 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r: 322 #if ($library.type == "paired" or $library.type == "paired_collection") and $output_aligned_reads_l and $output_aligned_reads_r:
324 #from os.path import splitext 323 #from os.path import splitext
325 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) ) 324 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
326 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l' 325 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
327 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r' 326 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
328 #end if 327 #end if
503 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See &quot;Other Options&quot; section of Help below for information"> 502 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See &quot;Other Options&quot; section of Help below for information">
504 <option value="yes">Yes</option> 503 <option value="yes">Yes</option>
505 <option value="no" selected="true">No</option> 504 <option value="no" selected="true">No</option>
506 </param> 505 </param>
507 <when value="yes"> 506 <when value="yes">
508 <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" label="Guarantee that output SAM records are printed in an order corresponding to the order of the reads in the original input file. If selected output file will not be coordinate sorted." help="--reorder; Default=False"/>
509 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/> 507 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/>
510 <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/> 508 <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/>
511 </when> 509 </when>
512 <when value="no"> 510 <when value="no">
513 <!-- do nothing --> 511 <!-- do nothing -->
661 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> 659 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
662 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> 660 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
663 <param name="own_file" value="bowtie2-ref.fasta" /> 661 <param name="own_file" value="bowtie2-ref.fasta" />
664 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> 662 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
665 </test> 663 </test>
666 <test expect_num_outputs="1"> 664 <test expect_num_outputs="3">
667 <!-- test on paired collection --> 665 <!-- test on list paired collection -->
668 <param name="type" value="paired_collection"/> 666 <param name="type" value="paired_collection"/>
669 <param name="paired_options_selector" value="no"/> 667 <param name="paired_options_selector" value="no"/>
670 <param name="unaligned_file" value="false"/> 668 <param name="unaligned_file" value="true"/>
671 <param name="analysis_type_selector" value="simple"/> 669 <param name="analysis_type_selector" value="simple"/>
672 <param name="source" value="history" /> 670 <param name="source" value="history" />
673 <param name="input_1"> 671 <param name="input_1">
674 <collection type="paired"> 672 <collection type="paired">
675 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> 673 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />