Mercurial > repos > devteam > bowtie2
comparison bowtie2_wrapper.xml @ 28:cd659e8cc5fa draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a"
author | iuc |
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date | Mon, 31 Jan 2022 08:31:43 +0000 |
parents | a6d65b0c67af |
children | f6877ad76b00 |
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27:a6d65b0c67af | 28:cd659e8cc5fa |
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1 <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="20.05"> | 1 <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="20.05"> |
2 <description>- map reads against reference genome</description> | 2 <description>- map reads against reference genome</description> |
3 <xrefs> | |
4 <xref type="bio.tools">bowtie2</xref> | |
5 </xrefs> | |
3 <macros> | 6 <macros> |
4 <import>bowtie2_macros.xml</import> | 7 <import>bowtie2_macros.xml</import> |
5 </macros> | 8 </macros> |
6 <requirements> | 9 <requirements> |
7 <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement> | 10 <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement> |
8 <requirement type="package" version="1.11">samtools</requirement> | 11 <requirement type="package" version="1.14">samtools</requirement> |
9 </requirements> | 12 </requirements> |
10 <version_command>bowtie2 --version</version_command> | 13 <version_command>bowtie2 --version</version_command> |
11 <command detect_errors="exit_code"><![CDATA[ | 14 <command detect_errors="exit_code"><![CDATA[ |
12 ## Use pipefail if available to quit with first non-zero exit code | 15 ## Use pipefail if available to quit with first non-zero exit code |
13 set -o | grep -q pipefail && set -o pipefail; | 16 set -o | grep -q pipefail && set -o pipefail; |
657 <param name="analysis_type_selector" value="simple"/> | 660 <param name="analysis_type_selector" value="simple"/> |
658 <param name="source" value="history" /> | 661 <param name="source" value="history" /> |
659 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> | 662 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
660 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> | 663 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> |
661 <param name="own_file" value="bowtie2-ref.fasta" /> | 664 <param name="own_file" value="bowtie2-ref.fasta" /> |
662 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> | 665 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> |
663 </test> | 666 </test> |
664 <test expect_num_outputs="3"> | 667 <test expect_num_outputs="3"> |
665 <!-- test on list paired collection --> | 668 <!-- test on list paired collection --> |
666 <param name="type" value="paired_collection"/> | 669 <param name="type" value="paired_collection"/> |
667 <param name="paired_options_selector" value="no"/> | 670 <param name="paired_options_selector" value="no"/> |
673 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> | 676 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> |
674 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> | 677 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> |
675 </collection> | 678 </collection> |
676 </param> | 679 </param> |
677 <param name="own_file" value="bowtie2-ref.fasta" /> | 680 <param name="own_file" value="bowtie2-ref.fasta" /> |
678 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> | 681 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> |
679 </test> | 682 </test> |
680 <test expect_num_outputs="1"> | 683 <test expect_num_outputs="1"> |
681 <!-- test on paired-end datasets with read group info --> | 684 <!-- test on paired-end datasets with read group info --> |
682 <param name="type" value="paired"/> | 685 <param name="type" value="paired"/> |
683 <param name="paired_options_selector" value="no"/> | 686 <param name="paired_options_selector" value="no"/> |
688 <param name="PL" value="CAPILLARY"/> | 691 <param name="PL" value="CAPILLARY"/> |
689 <param name="source" value="history" /> | 692 <param name="source" value="history" /> |
690 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> | 693 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
691 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> | 694 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> |
692 <param name="own_file" value="bowtie2-ref.fasta" /> | 695 <param name="own_file" value="bowtie2-ref.fasta" /> |
693 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/> | 696 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="4"/> |
694 </test> | 697 </test> |
695 <test expect_num_outputs="2"> | 698 <test expect_num_outputs="2"> |
696 <!-- test on paired-end datasets with stats output --> | 699 <!-- test on paired-end datasets with stats output --> |
697 <param name="type" value="paired"/> | 700 <param name="type" value="paired"/> |
698 <param name="paired_options_selector" value="no"/> | 701 <param name="paired_options_selector" value="no"/> |
701 <param name="source" value="history" /> | 704 <param name="source" value="history" /> |
702 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> | 705 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
703 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> | 706 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> |
704 <param name="own_file" value="bowtie2-ref.fasta" /> | 707 <param name="own_file" value="bowtie2-ref.fasta" /> |
705 <param name="save_mapping_stats" value="true" /> | 708 <param name="save_mapping_stats" value="true" /> |
706 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> | 709 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> |
707 <output name="mapping_stats"> | 710 <output name="mapping_stats"> |
708 <assert_contents> | 711 <assert_contents> |
709 <has_text text="of these" /> | 712 <has_text text="of these" /> |
710 </assert_contents> | 713 </assert_contents> |
711 </output> | 714 </output> |
720 <param name="ID" value="rg1"/> | 723 <param name="ID" value="rg1"/> |
721 <param name="PL" value="CAPILLARY"/> | 724 <param name="PL" value="CAPILLARY"/> |
722 <param name="source" value="history" /> | 725 <param name="source" value="history" /> |
723 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/> | 726 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/> |
724 <param name="own_file" value="bowtie2-ref.fasta" /> | 727 <param name="own_file" value="bowtie2-ref.fasta" /> |
725 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/> | 728 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="4"/> |
726 </test> | 729 </test> |
727 <test expect_num_outputs="1"> | 730 <test expect_num_outputs="1"> |
728 <!-- test on fastqsanger.gz paired-end datasets --> | 731 <!-- test on fastqsanger.gz paired-end datasets --> |
729 <param name="type" value="paired"/> | 732 <param name="type" value="paired"/> |
730 <param name="paired_options_selector" value="no"/> | 733 <param name="paired_options_selector" value="no"/> |
732 <param name="analysis_type_selector" value="simple"/> | 735 <param name="analysis_type_selector" value="simple"/> |
733 <param name="source" value="history" /> | 736 <param name="source" value="history" /> |
734 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/> | 737 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/> |
735 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/> | 738 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/> |
736 <param name="own_file" value="bowtie2-ref.fasta" /> | 739 <param name="own_file" value="bowtie2-ref.fasta" /> |
737 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> | 740 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> |
738 </test> | 741 </test> |
739 <test expect_num_outputs="1"> | 742 <test expect_num_outputs="1"> |
740 <!-- test on fastqsanger.bz2 paired-end datasets --> | 743 <!-- test on fastqsanger.bz2 paired-end datasets --> |
741 <param name="type" value="paired"/> | 744 <param name="type" value="paired"/> |
742 <param name="paired_options_selector" value="no"/> | 745 <param name="paired_options_selector" value="no"/> |
744 <param name="analysis_type_selector" value="simple"/> | 747 <param name="analysis_type_selector" value="simple"/> |
745 <param name="source" value="history" /> | 748 <param name="source" value="history" /> |
746 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/> | 749 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/> |
747 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/> | 750 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/> |
748 <param name="own_file" value="bowtie2-ref.fasta" /> | 751 <param name="own_file" value="bowtie2-ref.fasta" /> |
749 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> | 752 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> |
750 </test> | 753 </test> |
751 <test expect_num_outputs="1"> | 754 <test expect_num_outputs="1"> |
752 <!-- test on fasta paired-end datasets --> | 755 <!-- test on fasta paired-end datasets --> |
753 <param name="type" value="paired"/> | 756 <param name="type" value="paired"/> |
754 <param name="paired_options_selector" value="no"/> | 757 <param name="paired_options_selector" value="no"/> |
756 <param name="analysis_type_selector" value="simple"/> | 759 <param name="analysis_type_selector" value="simple"/> |
757 <param name="source" value="history" /> | 760 <param name="source" value="history" /> |
758 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> | 761 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> |
759 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> | 762 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> |
760 <param name="own_file" value="bowtie2-ref.fasta" /> | 763 <param name="own_file" value="bowtie2-ref.fasta" /> |
761 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/> | 764 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4"/> |
762 </test> | 765 </test> |
763 <test expect_num_outputs="1"> | 766 <test expect_num_outputs="1"> |
764 <!-- test on fasta paired-end datasets with bam_native as output --> | 767 <!-- test on fasta paired-end datasets with bam_native as output --> |
765 <param name="type" value="paired"/> | 768 <param name="type" value="paired"/> |
766 <param name="paired_options_selector" value="no"/> | 769 <param name="paired_options_selector" value="no"/> |