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comparison bowtie2_wrapper.xml @ 24:017aba02828d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 2c7869d210d1316e0eb3c9e9f926e1f18332c1ac
author iuc
date Thu, 04 Apr 2019 09:39:51 -0400
parents 17062a0decb7
children 749c918495f7
comparison
equal deleted inserted replaced
23:17062a0decb7 24:017aba02828d
1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.2" profile="18.01"> 1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.3" 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="2.3.4.1">bowtie2</requirement>
8 <requirement type="package" version="1.8">samtools</requirement> 8 <requirement type="package" version="1.9">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;
308 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''): 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 if $sam_options.reorder: 310 #else if $sam_options.reorder:
311 | samtools view -bS - -o '$output' 311 | samtools view -bS - -o '$output'
312 #else: 312 #else:
313 > '$output_sam' 313 > '$output'
314 #end if 314 #end if
315 315
316 ## rename unaligned sequence files 316 ## rename unaligned sequence files
317 #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 $output_unaligned_reads_r:
318 #from os.path import splitext 318 #from os.path import splitext
617 </when> 617 </when>
618 </conditional> 618 </conditional>
619 <expand macro="dbKeyActions" /> 619 <expand macro="dbKeyActions" />
620 </actions> 620 </actions>
621 </data> 621 </data>
622 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (BAM)"> 622 <data format="bam" name="output" label="${tool.name} on ${on_string}: alignments">
623 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
624 <change_format> 623 <change_format>
625 <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" /> 624 <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" />
625 <when input="sam_options.sam_opt" value="true" format="sam" />
626 </change_format> 626 </change_format>
627 <actions>
628 <conditional name="reference_genome.source">
629 <when value="indexed">
630 <action type="metadata" name="dbkey">
631 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
632 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
633 <filter type="param_value" ref="reference_genome.index" column="0"/>
634 </option>
635 </action>
636 </when>
637 <when value="history">
638 <action type="metadata" name="dbkey">
639 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
640 </action>
641 </when>
642 </conditional>
643 <expand macro="dbKeyActions" />
644 </actions>
645 </data>
646 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
647 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
648 <actions> 627 <actions>
649 <conditional name="reference_genome.source"> 628 <conditional name="reference_genome.source">
650 <when value="indexed"> 629 <when value="indexed">
651 <action type="metadata" name="dbkey"> 630 <action type="metadata" name="dbkey">
652 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> 631 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
670 <expand macro="dbKeyActions" /> 649 <expand macro="dbKeyActions" />
671 </actions> 650 </actions>
672 </data> 651 </data>
673 </outputs> 652 </outputs>
674 <tests> 653 <tests>
675 <test> 654 <test expect_num_outputs="1">
676 <!-- test on paired-end datasets --> 655 <!-- test on paired-end datasets -->
677 <param name="type" value="paired"/> 656 <param name="type" value="paired"/>
678 <param name="paired_options_selector" value="no"/> 657 <param name="paired_options_selector" value="no"/>
679 <param name="unaligned_file" value="false"/> 658 <param name="unaligned_file" value="false"/>
680 <param name="analysis_type_selector" value="simple"/> 659 <param name="analysis_type_selector" value="simple"/>
682 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> 661 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
683 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> 662 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
684 <param name="own_file" value="bowtie2-ref.fasta" /> 663 <param name="own_file" value="bowtie2-ref.fasta" />
685 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> 664 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
686 </test> 665 </test>
687 <test> 666 <test expect_num_outputs="1">
688 <!-- test on paired collection --> 667 <!-- test on paired collection -->
689 <param name="type" value="paired_collection"/> 668 <param name="type" value="paired_collection"/>
690 <param name="paired_options_selector" value="no"/> 669 <param name="paired_options_selector" value="no"/>
691 <param name="unaligned_file" value="false"/> 670 <param name="unaligned_file" value="false"/>
692 <param name="analysis_type_selector" value="simple"/> 671 <param name="analysis_type_selector" value="simple"/>
698 </collection> 677 </collection>
699 </param> 678 </param>
700 <param name="own_file" value="bowtie2-ref.fasta" /> 679 <param name="own_file" value="bowtie2-ref.fasta" />
701 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> 680 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
702 </test> 681 </test>
703 <test> 682 <test expect_num_outputs="1">
704 <!-- test on paired-end datasets with read group info --> 683 <!-- test on paired-end datasets with read group info -->
705 <param name="type" value="paired"/> 684 <param name="type" value="paired"/>
706 <param name="paired_options_selector" value="no"/> 685 <param name="paired_options_selector" value="no"/>
707 <param name="unaligned_file" value="false"/> 686 <param name="unaligned_file" value="false"/>
708 <param name="analysis_type_selector" value="simple"/> 687 <param name="analysis_type_selector" value="simple"/>
713 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> 692 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
714 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> 693 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
715 <param name="own_file" value="bowtie2-ref.fasta" /> 694 <param name="own_file" value="bowtie2-ref.fasta" />
716 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/> 695 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
717 </test> 696 </test>
718 <test> 697 <test expect_num_outputs="2">
719 <!-- test on paired-end datasets with stats output --> 698 <!-- test on paired-end datasets with stats output -->
720 <param name="type" value="paired"/> 699 <param name="type" value="paired"/>
721 <param name="paired_options_selector" value="no"/> 700 <param name="paired_options_selector" value="no"/>
722 <param name="unaligned_file" value="false"/> 701 <param name="unaligned_file" value="false"/>
723 <param name="analysis_type_selector" value="simple"/> 702 <param name="analysis_type_selector" value="simple"/>
731 <assert_contents> 710 <assert_contents>
732 <has_text text="of these" /> 711 <has_text text="of these" />
733 </assert_contents> 712 </assert_contents>
734 </output> 713 </output>
735 </test> 714 </test>
736 <test> 715 <test expect_num_outputs="1">
737 <!-- test on interleaved dataset --> 716 <!-- test on interleaved dataset -->
738 <param name="type" value="paired_interleaved"/> 717 <param name="type" value="paired_interleaved"/>
739 <!-- <param name="paired_options_selector" value="no"/> --> 718 <!-- <param name="paired_options_selector" value="no"/> -->
740 <param name="unaligned_file" value="false"/> 719 <param name="unaligned_file" value="false"/>
741 <param name="analysis_type_selector" value="simple"/> 720 <param name="analysis_type_selector" value="simple"/>
745 <param name="source" value="history" /> 724 <param name="source" value="history" />
746 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/> 725 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
747 <param name="own_file" value="bowtie2-ref.fasta" /> 726 <param name="own_file" value="bowtie2-ref.fasta" />
748 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/> 727 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/>
749 </test> 728 </test>
750 <test> 729 <test expect_num_outputs="1">
751 <!-- test on fastqsanger.gz paired-end datasets --> 730 <!-- test on fastqsanger.gz paired-end datasets -->
752 <param name="type" value="paired"/> 731 <param name="type" value="paired"/>
753 <param name="paired_options_selector" value="no"/> 732 <param name="paired_options_selector" value="no"/>
754 <param name="unaligned_file" value="false"/> 733 <param name="unaligned_file" value="false"/>
755 <param name="analysis_type_selector" value="simple"/> 734 <param name="analysis_type_selector" value="simple"/>
757 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/> 736 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
758 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/> 737 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
759 <param name="own_file" value="bowtie2-ref.fasta" /> 738 <param name="own_file" value="bowtie2-ref.fasta" />
760 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> 739 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
761 </test> 740 </test>
762 <test> 741 <test expect_num_outputs="1">
763 <!-- test on fastqsanger.bz2 paired-end datasets --> 742 <!-- test on fastqsanger.bz2 paired-end datasets -->
764 <param name="type" value="paired"/> 743 <param name="type" value="paired"/>
765 <param name="paired_options_selector" value="no"/> 744 <param name="paired_options_selector" value="no"/>
766 <param name="unaligned_file" value="false"/> 745 <param name="unaligned_file" value="false"/>
767 <param name="analysis_type_selector" value="simple"/> 746 <param name="analysis_type_selector" value="simple"/>
769 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/> 748 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
770 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/> 749 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
771 <param name="own_file" value="bowtie2-ref.fasta" /> 750 <param name="own_file" value="bowtie2-ref.fasta" />
772 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> 751 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
773 </test> 752 </test>
774 <test> 753 <test expect_num_outputs="1">
775 <!-- test on fasta paired-end datasets --> 754 <!-- test on fasta paired-end datasets -->
776 <param name="type" value="paired"/> 755 <param name="type" value="paired"/>
777 <param name="paired_options_selector" value="no"/> 756 <param name="paired_options_selector" value="no"/>
778 <param name="unaligned_file" value="false"/> 757 <param name="unaligned_file" value="false"/>
779 <param name="analysis_type_selector" value="simple"/> 758 <param name="analysis_type_selector" value="simple"/>
781 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> 760 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
782 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> 761 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
783 <param name="own_file" value="bowtie2-ref.fasta" /> 762 <param name="own_file" value="bowtie2-ref.fasta" />
784 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/> 763 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
785 </test> 764 </test>
786 <test> 765 <test expect_num_outputs="1">
787 <!-- test on fasta paired-end datasets with bam_native as output --> 766 <!-- test on fasta paired-end datasets with bam_native as output -->
788 <param name="type" value="paired"/> 767 <param name="type" value="paired"/>
789 <param name="paired_options_selector" value="no"/> 768 <param name="paired_options_selector" value="no"/>
790 <param name="unaligned_file" value="false"/> 769 <param name="unaligned_file" value="false"/>
791 <param name="analysis_type_selector" value="simple"/> 770 <param name="analysis_type_selector" value="simple"/>
794 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> 773 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
795 <param name="own_file" value="bowtie2-ref.fasta" /> 774 <param name="own_file" value="bowtie2-ref.fasta" />
796 <param name="sam_options_selector" value="yes" /> 775 <param name="sam_options_selector" value="yes" />
797 <param name="reorder" value="true" /> 776 <param name="reorder" value="true" />
798 <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/> 777 <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/>
778 </test>
779 <test expect_num_outputs="1">
780 <!-- test on fasta paired-end datasets with sam as output -->
781 <param name="type" value="paired"/>
782 <param name="paired_options_selector" value="no"/>
783 <param name="unaligned_file" value="false"/>
784 <param name="analysis_type_selector" value="simple"/>
785 <param name="source" value="history" />
786 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
787 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
788 <param name="own_file" value="bowtie2-ref.fasta" />
789 <param name="sam_options_selector" value="yes" />
790 <param name="sam_options|sam_opt" value="true" />
791 <output name="output" ftype="sam">
792 <assert_contents>
793 <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" />
794 </assert_contents>
795 </output>
799 </test> 796 </test>
800 </tests> 797 </tests>
801 <help><![CDATA[ 798 <help><![CDATA[
802 **Bowtie2 Overview** 799 **Bowtie2 Overview**
803 800