Mercurial > repos > devteam > bowtie2

comparison bowtie2_wrapper.xml @ 22:c3dd1aeb7d07 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit fcc7b4c9511c40ae06cd88dfa308201f63d4ac32
author iuc
date Thu, 12 Apr 2018 17:42:40 -0400
parents 3ba8d4563129
children 17062a0decb7
comparison
equal deleted inserted replaced
21:3ba8d4563129 22:c3dd1aeb7d07
1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.1" profile="17.01"> 1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.2" 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>
7 <requirement type="package" version="2.3.4">bowtie2</requirement> 7 <requirement type="package" version="2.3.4">bowtie2</requirement>
8 <requirement type="package" version="1.6">samtools</requirement> 8 <requirement type="package" version="1.8">samtools</requirement>
9 </requirements> 9 </requirements>
10 <version_command>bowtie2 --version</version_command> 10 <version_command>bowtie2 --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 ## Use pipefail if available to quit with first non-zero exit code 12 ## Use pipefail if available to quit with first non-zero exit code
13 set -o | grep -q pipefail && set -o pipefail; 13 set -o | grep -q pipefail && set -o pipefail;
278 278
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
284 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
285 ${analysis_type.sam_options.no_unal}
286 ${analysis_type.sam_options.omit_sec_seq}
287 ${analysis_type.sam_options.sam_no_qname_trunc}
288 ${analysis_type.sam_options.xeq}
289 ${analysis_type.sam_options.soft_clipped_unmapped_tlen}
290 #end if
291
292 #if str( $analysis_type.other_options.other_options_selector ) == "yes": 283 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
293 ${analysis_type.other_options.reorder} 284 ${analysis_type.other_options.reorder}
294 ${analysis_type.other_options.non_deterministic} 285 ${analysis_type.other_options.non_deterministic}
295 --seed ${analysis_type.other_options.seed} 286 --seed ${analysis_type.other_options.seed}
296 #end if 287 #end if
297 288
298 #elif str( $analysis_type.analysis_type_selector ) == "cline": 289 #elif str( $analysis_type.analysis_type_selector ) == "cline":
299 ${analysis_type.cline} 290 ${analysis_type.cline}
300 #end if 291 #end if
301 292
293 #if str( $sam_options.sam_options_selector ) == "yes":
294 ${sam_options.no_unal}
295 ${sam_options.omit_sec_seq}
296 ${sam_options.sam_no_qname_trunc}
297 ${sam_options.xeq}
298 ${sam_options.soft_clipped_unmapped_tlen}
299 ${sam_options.reorder}
300 #end if
301
302 ## mapping stats (i.e. stderr from bowtie2) 302 ## mapping stats (i.e. stderr from bowtie2)
303 #if $save_mapping_stats 303 #if $save_mapping_stats
304 2> '$mapping_stats' 304 2> '$mapping_stats'
305 #end if 305 #end if
306 306
307 ## output file 307 ## output file
308 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ): 308 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
309 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output' 309 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
310 #else 310 #else if $sam_options.reorder:
311 | samtools view -bS - -o '$output'
312 #else:
311 > '$output_sam' 313 > '$output_sam'
312 #end if 314 #end if
313 315
314 ## rename unaligned sequence files 316 ## rename unaligned sequence files
315 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: 317 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
495 </when> 497 </when>
496 <when value="no"> 498 <when value="no">
497 <!-- do nothing --> 499 <!-- do nothing -->
498 </when> 500 </when>
499 </conditional> 501 </conditional>
500 <conditional name="sam_options">
501 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
502 <option value="yes">Yes</option>
503 <option value="no" selected="true">No</option>
504 </param>
505 <when value="yes">
506 <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"/>
507 <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"/>
508 <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"/>
509 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
510 <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"/>
511 </when>
512 <when value="no">
513 <!-- do nothing -->
514 </when>
515 </conditional>
516 <conditional name="other_options"> 502 <conditional name="other_options">
517 <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"> 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">
518 <option value="yes">Yes</option> 504 <option value="yes">Yes</option>
519 <option value="no" selected="true">No</option> 505 <option value="no" selected="true">No</option>
520 </param> 506 </param>
521 <when value="yes"> 507 <when value="yes">
522 <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" help="--reorder; Default=False"/> 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"/>
523 <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"/> 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"/>
524 <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"/> 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"/>
525 </when> 511 </when>
526 <when value="no"> 512 <when value="no">
527 <!-- do nothing --> 513 <!-- do nothing -->
528 </when> 514 </when>
529 </conditional> 515 </conditional>
516 </when>
517 </conditional>
518 <conditional name="sam_options">
519 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
520 <option value="yes">Yes</option>
521 <option value="no" selected="true">No</option>
522 </param>
523 <when value="yes">
530 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/> 524 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
525 <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"/>
526 <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"/>
527 <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"/>
528 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
529 <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"/>
530 <param name="reorder" argument="--reorder" type="boolean" truevalue="--reorder" falsevalue=""
531 label="Reorder output to reflect order of the input file"
532 help="Reorder guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when -p is set greater than 1." />
531 </when> 533 </when>
534 <when value="no"/>
532 </conditional> 535 </conditional>
533 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" /> 536 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
534 </inputs> 537 </inputs>
535 <!-- define outputs --> 538 <!-- define outputs -->
536 <outputs> 539 <outputs>
610 </action> 613 </action>
611 </when> 614 </when>
612 </conditional> 615 </conditional>
613 </actions> 616 </actions>
614 </data> 617 </data>
615 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)"> 618 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (BAM)">
616 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter> 619 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
620 <change_format>
621 <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" />
622 </change_format>
617 <actions> 623 <actions>
618 <conditional name="reference_genome.source"> 624 <conditional name="reference_genome.source">
619 <when value="indexed"> 625 <when value="indexed">
620 <action type="metadata" name="dbkey"> 626 <action type="metadata" name="dbkey">
621 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> 627 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
766 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> 772 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
767 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> 773 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
768 <param name="own_file" value="bowtie2-ref.fasta" /> 774 <param name="own_file" value="bowtie2-ref.fasta" />
769 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/> 775 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
770 </test> 776 </test>
777 <test>
778 <!-- test on fasta paired-end datasets with bam_native as output -->
779 <param name="type" value="paired"/>
780 <param name="paired_options_selector" value="no"/>
781 <param name="unaligned_file" value="false"/>
782 <param name="analysis_type_selector" value="simple"/>
783 <param name="source" value="history" />
784 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
785 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
786 <param name="own_file" value="bowtie2-ref.fasta" />
787 <param name="sam_options_selector" value="yes" />
788 <param name="reorder" value="true" />
789 <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/>
790 </test>
771 </tests> 791 </tests>
772 <help><![CDATA[ 792 <help><![CDATA[
773 **Bowtie2 Overview** 793 **Bowtie2 Overview**
774 794
775 Bowtie2_ is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Galaxy wrapper for Bowtie 2 outputs alignments in `BAM format`_, enabling interoperation with a large number of other tools available at this site. 795 Bowtie2_ is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Galaxy wrapper for Bowtie 2 outputs alignments in `BAM format`_, enabling interoperation with a large number of other tools available at this site.