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comparison bowtie2_wrapper.xml @ 29:f6877ad76b00 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
author iuc
date Wed, 06 Jul 2022 10:26:09 +0000
parents cd659e8cc5fa
children 03e9b2fbc005
comparison
equal deleted inserted replaced
28:cd659e8cc5fa 29:f6877ad76b00
1 <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="20.05"> 1 <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy1" profile="20.05">
2 <description>- map reads against reference genome</description> 2 <description>- map reads against reference genome</description>
3 <macros>
4 <import>bowtie2_macros.xml</import>
5 </macros>
3 <xrefs> 6 <xrefs>
4 <xref type="bio.tools">bowtie2</xref> 7 <xref type="bio.tools">bowtie2</xref>
5 </xrefs> 8 </xrefs>
6 <macros>
7 <import>bowtie2_macros.xml</import>
8 </macros>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
11 <requirement type="package" version="1.14">samtools</requirement> 11 <requirement type="package" version="1.14">samtools</requirement>
12 </requirements> 12 </requirements>
13 <version_command>bowtie2 --version</version_command> 13 <version_command>bowtie2 --version</version_command>
660 <param name="analysis_type_selector" value="simple"/> 660 <param name="analysis_type_selector" value="simple"/>
661 <param name="source" value="history" /> 661 <param name="source" value="history" />
662 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> 662 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
663 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> 663 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
664 <param name="own_file" value="bowtie2-ref.fasta" /> 664 <param name="own_file" value="bowtie2-ref.fasta" />
665 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> 665 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
666 <metadata name="sort_order" value="coordinate"/>
667 </output>
666 </test> 668 </test>
667 <test expect_num_outputs="3"> 669 <test expect_num_outputs="3">
668 <!-- test on list paired collection --> 670 <!-- test on list paired collection -->
669 <param name="type" value="paired_collection"/> 671 <param name="type" value="paired_collection"/>
670 <param name="paired_options_selector" value="no"/> 672 <param name="paired_options_selector" value="no"/>
676 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> 678 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
677 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> 679 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
678 </collection> 680 </collection>
679 </param> 681 </param>
680 <param name="own_file" value="bowtie2-ref.fasta" /> 682 <param name="own_file" value="bowtie2-ref.fasta" />
681 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> 683 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
684 <metadata name="sort_order" value="coordinate"/>
685 </output>
682 </test> 686 </test>
683 <test expect_num_outputs="1"> 687 <test expect_num_outputs="1">
684 <!-- test on paired-end datasets with read group info --> 688 <!-- test on paired-end datasets with read group info -->
685 <param name="type" value="paired"/> 689 <param name="type" value="paired"/>
686 <param name="paired_options_selector" value="no"/> 690 <param name="paired_options_selector" value="no"/>
691 <param name="PL" value="CAPILLARY"/> 695 <param name="PL" value="CAPILLARY"/>
692 <param name="source" value="history" /> 696 <param name="source" value="history" />
693 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> 697 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
694 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> 698 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
695 <param name="own_file" value="bowtie2-ref.fasta" /> 699 <param name="own_file" value="bowtie2-ref.fasta" />
696 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="4"/> 700 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="4" sort="true">
701 <metadata name="sort_order" value="coordinate"/>
702 </output>
697 </test> 703 </test>
698 <test expect_num_outputs="2"> 704 <test expect_num_outputs="2">
699 <!-- test on paired-end datasets with stats output --> 705 <!-- test on paired-end datasets with stats output -->
700 <param name="type" value="paired"/> 706 <param name="type" value="paired"/>
701 <param name="paired_options_selector" value="no"/> 707 <param name="paired_options_selector" value="no"/>
704 <param name="source" value="history" /> 710 <param name="source" value="history" />
705 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> 711 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
706 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> 712 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
707 <param name="own_file" value="bowtie2-ref.fasta" /> 713 <param name="own_file" value="bowtie2-ref.fasta" />
708 <param name="save_mapping_stats" value="true" /> 714 <param name="save_mapping_stats" value="true" />
709 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> 715 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
716 <metadata name="sort_order" value="coordinate"/>
717 </output>
710 <output name="mapping_stats"> 718 <output name="mapping_stats">
711 <assert_contents> 719 <assert_contents>
712 <has_text text="of these" /> 720 <has_text text="of these" />
713 </assert_contents> 721 </assert_contents>
714 </output> 722 </output>
723 <param name="ID" value="rg1"/> 731 <param name="ID" value="rg1"/>
724 <param name="PL" value="CAPILLARY"/> 732 <param name="PL" value="CAPILLARY"/>
725 <param name="source" value="history" /> 733 <param name="source" value="history" />
726 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/> 734 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
727 <param name="own_file" value="bowtie2-ref.fasta" /> 735 <param name="own_file" value="bowtie2-ref.fasta" />
728 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="4"/> 736 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="4" sort="true">
737 <metadata name="sort_order" value="coordinate"/>
738 </output>
729 </test> 739 </test>
730 <test expect_num_outputs="1"> 740 <test expect_num_outputs="1">
731 <!-- test on fastqsanger.gz paired-end datasets --> 741 <!-- test on fastqsanger.gz paired-end datasets -->
732 <param name="type" value="paired"/> 742 <param name="type" value="paired"/>
733 <param name="paired_options_selector" value="no"/> 743 <param name="paired_options_selector" value="no"/>
735 <param name="analysis_type_selector" value="simple"/> 745 <param name="analysis_type_selector" value="simple"/>
736 <param name="source" value="history" /> 746 <param name="source" value="history" />
737 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/> 747 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
738 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/> 748 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
739 <param name="own_file" value="bowtie2-ref.fasta" /> 749 <param name="own_file" value="bowtie2-ref.fasta" />
740 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> 750 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
751 <metadata name="sort_order" value="coordinate"/>
752 </output>
741 </test> 753 </test>
742 <test expect_num_outputs="1"> 754 <test expect_num_outputs="1">
743 <!-- test on fastqsanger.bz2 paired-end datasets --> 755 <!-- test on fastqsanger.bz2 paired-end datasets -->
744 <param name="type" value="paired"/> 756 <param name="type" value="paired"/>
745 <param name="paired_options_selector" value="no"/> 757 <param name="paired_options_selector" value="no"/>
747 <param name="analysis_type_selector" value="simple"/> 759 <param name="analysis_type_selector" value="simple"/>
748 <param name="source" value="history" /> 760 <param name="source" value="history" />
749 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/> 761 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
750 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/> 762 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
751 <param name="own_file" value="bowtie2-ref.fasta" /> 763 <param name="own_file" value="bowtie2-ref.fasta" />
752 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/> 764 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
765 <metadata name="sort_order" value="coordinate"/>
766 </output>
753 </test> 767 </test>
754 <test expect_num_outputs="1"> 768 <test expect_num_outputs="1">
755 <!-- test on fasta paired-end datasets --> 769 <!-- test on fasta paired-end datasets -->
756 <param name="type" value="paired"/> 770 <param name="type" value="paired"/>
757 <param name="paired_options_selector" value="no"/> 771 <param name="paired_options_selector" value="no"/>
759 <param name="analysis_type_selector" value="simple"/> 773 <param name="analysis_type_selector" value="simple"/>
760 <param name="source" value="history" /> 774 <param name="source" value="history" />
761 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> 775 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
762 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> 776 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
763 <param name="own_file" value="bowtie2-ref.fasta" /> 777 <param name="own_file" value="bowtie2-ref.fasta" />
764 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4"/> 778 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4" sort="true">
779 <metadata name="sort_order" value="coordinate"/>
780 </output>
765 </test> 781 </test>
766 <test expect_num_outputs="1"> 782 <test expect_num_outputs="1">
767 <!-- test on fasta paired-end datasets with bam_native as output --> 783 <!-- test on fasta paired-end datasets with bam_native as output -->
768 <param name="type" value="paired"/> 784 <param name="type" value="paired"/>
769 <param name="paired_options_selector" value="no"/> 785 <param name="paired_options_selector" value="no"/>
773 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> 789 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
774 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> 790 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
775 <param name="own_file" value="bowtie2-ref.fasta" /> 791 <param name="own_file" value="bowtie2-ref.fasta" />
776 <param name="sam_options_selector" value="yes" /> 792 <param name="sam_options_selector" value="yes" />
777 <param name="reorder" value="true" /> 793 <param name="reorder" value="true" />
778 <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/> 794 <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" lines_diff="4">
795 <metadata name="sort_order" value="unsorted"/>
796 </output>
779 </test> 797 </test>
780 <test expect_num_outputs="1"> 798 <test expect_num_outputs="1">
781 <!-- test on fasta paired-end datasets with sam as output --> 799 <!-- test on fasta paired-end datasets with sam as output -->
782 <param name="type" value="paired"/> 800 <param name="type" value="paired"/>
783 <param name="paired_options_selector" value="no"/> 801 <param name="paired_options_selector" value="no"/>
788 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> 806 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
789 <param name="own_file" value="bowtie2-ref.fasta" /> 807 <param name="own_file" value="bowtie2-ref.fasta" />
790 <param name="sam_options_selector" value="yes" /> 808 <param name="sam_options_selector" value="yes" />
791 <param name="sam_options|sam_opt" value="true" /> 809 <param name="sam_options|sam_opt" value="true" />
792 <output name="output" ftype="sam"> 810 <output name="output" ftype="sam">
811 <metadata name="sort_order" value="unsorted"/>
793 <assert_contents> 812 <assert_contents>
794 <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" /> 813 <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" />
795 </assert_contents> 814 </assert_contents>
796 </output> 815 </output>
797 </test> 816 </test>