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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03
author iuc
date Wed, 06 Jul 2022 10:26:44 +0000
parents 6c19daec423d
children
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30:6c19daec423d 31:f4af63aaf57a
1 <tool id="hisat2" name="HISAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 1 <tool id="hisat2" name="HISAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>A fast and sensitive alignment program</description> 2 <description>A fast and sensitive alignment program</description>
3 <macros> 3 <macros>
4 <import>hisat2_macros.xml</import> 4 <import>hisat2_macros.xml</import>
5 </macros> 5 </macros>
6 <xrefs>
7 <xref type="bio.tools">hisat2</xref>
8 </xrefs>
6 <requirements> 9 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">hisat2</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">hisat2</requirement>
8 <requirement type="package" version="1.12">samtools</requirement> 11 <requirement type="package" version="1.12">samtools</requirement>
9 <requirement type="package" version="1.3">seqtk</requirement> 12 <requirement type="package" version="1.3">seqtk</requirement>
10 </requirements> 13 </requirements>
559 <when value="defaults" /> 562 <when value="defaults" />
560 <when value="advanced"> 563 <when value="advanced">
561 <param name="no_unal" argument="--no-unal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress SAM records for reads that failed to align." help="Default: false"/> 564 <param name="no_unal" argument="--no-unal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress SAM records for reads that failed to align." help="Default: false"/>
562 <conditional name="read_groups"> 565 <conditional name="read_groups">
563 <param name="rg_labels" type="select" label="Edit Read Group IDs"> 566 <param name="rg_labels" type="select" label="Edit Read Group IDs">
564 <option value="No" /> 567 <option value="No">No</option>
565 <option value="Yes" /> 568 <option value="Yes">Yes</option>
566 </param> 569 </param>
567 <when value="No"/> 570 <when value="No"/>
568 <when value="Yes"> 571 <when value="Yes">
569 <param name="rg_id" argument="--rg-id" type="text" value="read_group" label="Read Group ID" help="Set the read group ID to the value set here. This causes the SAM @RG header line to be printed, with this input value as the value associated with the ID: tag. It also causes the RG:Z: extra field to be attached to each SAM output record, with value set to the value set here." /> 572 <param name="rg_id" argument="--rg-id" type="text" value="read_group" label="Read Group ID" help="Set the read group ID to the value set here. This causes the SAM @RG header line to be printed, with this input value as the value associated with the ID: tag. It also causes the RG:Z: extra field to be attached to each SAM output record, with value set to the value set here." />
570 <repeat name="read_groups" title="Read Groups text"> 573 <repeat name="read_groups" title="Read Groups text">
756 <param name="history_item" ftype="fasta" value="phiX.fa" /> 759 <param name="history_item" ftype="fasta" value="phiX.fa" />
757 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" /> 760 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
758 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" /> 761 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
759 <param name="adv|reporting_options|reporting_options_selector" value="advanced"/> 762 <param name="adv|reporting_options|reporting_options_selector" value="advanced"/>
760 <param name="novel_splicesite_outfile" value="false" /> 763 <param name="novel_splicesite_outfile" value="false" />
761 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> 764 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" >
765 <metadata name="sort_order" value="coordinate"/>
766 </output>
762 </test> 767 </test>
763 <!-- Ensure advanced scoring options work --> 768 <!-- Ensure advanced scoring options work -->
764 <test expect_num_outputs="1" > 769 <test expect_num_outputs="1" >
765 <param name="type" value="paired" /> 770 <param name="type" value="paired" />
766 <param name="source" value="history" /> 771 <param name="source" value="history" />
767 <param name="history_item" ftype="fasta" value="phiX.fa" /> 772 <param name="history_item" ftype="fasta" value="phiX.fa" />
768 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" /> 773 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
769 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" /> 774 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
770 <param name="adv|scoring_options|coefficient" value="-0.3"/> 775 <param name="adv|scoring_options|coefficient" value="-0.3"/>
771 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> 776 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >
777 <metadata name="sort_order" value="coordinate"/>
778 </output>
772 </test> 779 </test>
773 <!-- Ensure built-in reference works --> 780 <!-- Ensure built-in reference works -->
774 <test expect_num_outputs="1"> 781 <test expect_num_outputs="1">
775 <param name="type" value="paired" /> 782 <param name="type" value="paired" />
776 <param name="source" value="indexed" /> 783 <param name="source" value="indexed" />
777 <param name="input_1" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_forward.fastq" /> 784 <param name="input_1" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_forward.fastq" />
778 <param name="input_2" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_reverse.fastq" /> 785 <param name="input_2" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_reverse.fastq" />
779 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> 786 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >
787 <metadata name="sort_order" value="coordinate"/>
788 </output>
780 </test> 789 </test>
781 <!-- Ensure trimming works --> 790 <!-- Ensure trimming works -->
782 <test expect_num_outputs="1"> 791 <test expect_num_outputs="1">
783 <param name="type" value="paired" /> 792 <param name="type" value="paired" />
784 <param name="source" value="history" /> 793 <param name="source" value="history" />
786 <param name="input_options_selector" value="advanced" /> 795 <param name="input_options_selector" value="advanced" />
787 <param name="trim3" value="15" /> 796 <param name="trim3" value="15" />
788 <param name="trim5" value="15" /> 797 <param name="trim5" value="15" />
789 <param name="input_1" ftype="fastqsanger" value="hisat_input_2_forward.fastq" /> 798 <param name="input_1" ftype="fastqsanger" value="hisat_input_2_forward.fastq" />
790 <param name="input_2" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" /> 799 <param name="input_2" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />
791 <output name="output_alignments" file="hisat_output_2.bam" ftype="bam" lines_diff="2" /> 800 <output name="output_alignments" file="hisat_output_2.bam" ftype="bam" lines_diff="2" sort="true" >
801 <metadata name="sort_order" value="coordinate"/>
802 </output>
792 </test> 803 </test>
793 <!-- Ensure paired options works --> 804 <!-- Ensure paired options works -->
794 <test expect_num_outputs="1"> 805 <test expect_num_outputs="1">
795 <param name="type" value="paired" /> 806 <param name="type" value="paired" />
796 <param name="source" value="history" /> 807 <param name="source" value="history" />
801 <param name="input_1" ftype="fastqsanger" value="hisat_input_2_forward.fastq" /> 812 <param name="input_1" ftype="fastqsanger" value="hisat_input_2_forward.fastq" />
802 <param name="input_2" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" /> 813 <param name="input_2" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />
803 <param name="paired_options_selector" value="advanced" /> 814 <param name="paired_options_selector" value="advanced" />
804 <param name="no_mixed" value="True" /> 815 <param name="no_mixed" value="True" />
805 <param name="no_discordant" value="True" /> 816 <param name="no_discordant" value="True" />
806 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> 817 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" sort="true" >
818 <metadata name="sort_order" value="coordinate"/>
819 </output>
807 </test> 820 </test>
808 <!-- Ensure single unaligned output works --> 821 <!-- Ensure single unaligned output works -->
809 <test expect_num_outputs="2"> 822 <test expect_num_outputs="2">
810 <param name="type" value="single" /> 823 <param name="type" value="single" />
811 <param name="source" value="history" /> 824 <param name="source" value="history" />
840 <param name="input_1" ftype="fastqsanger.gz" value="hisat_input_2_forward.fastq.gz" /> 853 <param name="input_1" ftype="fastqsanger.gz" value="hisat_input_2_forward.fastq.gz" />
841 <param name="input_2" ftype="fastqsanger.gz" value="hisat_input_2_reverse.fastq.gz" /> 854 <param name="input_2" ftype="fastqsanger.gz" value="hisat_input_2_reverse.fastq.gz" />
842 <param name="paired_options_selector" value="advanced" /> 855 <param name="paired_options_selector" value="advanced" />
843 <param name="no_mixed" value="True" /> 856 <param name="no_mixed" value="True" />
844 <param name="no_discordant" value="True" /> 857 <param name="no_discordant" value="True" />
845 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> 858 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" sort="true" >
859 <metadata name="sort_order" value="coordinate"/>
860 </output>
846 </test> 861 </test>
847 <!-- Ensure fastqsanger.bz2 works --> 862 <!-- Ensure fastqsanger.bz2 works -->
848 <test expect_num_outputs="1"> 863 <test expect_num_outputs="1">
849 <param name="type" value="paired" /> 864 <param name="type" value="paired" />
850 <param name="source" value="history" /> 865 <param name="source" value="history" />
855 <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_2_forward.fastq.bz2" /> 870 <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_2_forward.fastq.bz2" />
856 <param name="input_2" ftype="fastqsanger.bz2" value="hisat_input_2_reverse.fastq.bz2" /> 871 <param name="input_2" ftype="fastqsanger.bz2" value="hisat_input_2_reverse.fastq.bz2" />
857 <param name="paired_options_selector" value="advanced" /> 872 <param name="paired_options_selector" value="advanced" />
858 <param name="no_mixed" value="True" /> 873 <param name="no_mixed" value="True" />
859 <param name="no_discordant" value="True" /> 874 <param name="no_discordant" value="True" />
860 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> 875 <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" sort="true" >
876 <metadata name="sort_order" value="coordinate"/>
877 </output>
861 </test> 878 </test>
862 <!-- Ensure paired strandness works --> 879 <!-- Ensure paired strandness works -->
863 <test expect_num_outputs="1"> 880 <test expect_num_outputs="1">
864 <param name="type" value="paired" /> 881 <param name="type" value="paired" />
865 <param name="source" value="history" /> 882 <param name="source" value="history" />
866 <param name="history_item" ftype="fasta" value="phiX.fa" /> 883 <param name="history_item" ftype="fasta" value="phiX.fa" />
867 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" /> 884 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
868 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" /> 885 <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
869 <param name="rna_strandness" value="FR" /> 886 <param name="rna_strandness" value="FR" />
870 <output name="output_alignments" file="hisat_output_4.bam" ftype="bam" lines_diff="2" /> 887 <output name="output_alignments" file="hisat_output_4.bam" ftype="bam" lines_diff="2" sort="true" >
888 <metadata name="sort_order" value="coordinate"/>
889 </output>
871 </test> 890 </test>
872 <!-- Ensure summary file output works --> 891 <!-- Ensure summary file output works -->
873 <test expect_num_outputs="2"> 892 <test expect_num_outputs="2">
874 <param name="type" value="single" /> 893 <param name="type" value="single" />
875 <param name="source" value="history" /> 894 <param name="source" value="history" />
884 <test expect_num_outputs="1" > 903 <test expect_num_outputs="1" >
885 <param name="type" value="paired_interleaved" /> 904 <param name="type" value="paired_interleaved" />
886 <param name="source" value="history" /> 905 <param name="source" value="history" />
887 <param name="history_item" ftype="fasta" value="phiX.fa" /> 906 <param name="history_item" ftype="fasta" value="phiX.fa" />
888 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_interleaved.fastq" /> 907 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_interleaved.fastq" />
889 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> 908 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >
909 <metadata name="sort_order" value="coordinate"/>
910 </output>
890 </test> 911 </test>
891 <!-- Ensure interleaved bz input works --> 912 <!-- Ensure interleaved bz input works -->
892 <test expect_num_outputs="1" > 913 <test expect_num_outputs="1" >
893 <param name="type" value="paired_interleaved" /> 914 <param name="type" value="paired_interleaved" />
894 <param name="source" value="history" /> 915 <param name="source" value="history" />
895 <param name="history_item" ftype="fasta" value="phiX.fa" /> 916 <param name="history_item" ftype="fasta" value="phiX.fa" />
896 <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_1_interleaved.fastq.bz2" /> 917 <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_1_interleaved.fastq.bz2" />
897 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> 918 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >
919 <metadata name="sort_order" value="coordinate"/>
920 </output>
898 </test> 921 </test>
899 <!-- Ensure interleaved gz input works --> 922 <!-- Ensure interleaved gz input works -->
900 <test expect_num_outputs="1" > 923 <test expect_num_outputs="1" >
901 <param name="type" value="paired_interleaved" /> 924 <param name="type" value="paired_interleaved" />
902 <param name="source" value="history" /> 925 <param name="source" value="history" />
903 <param name="history_item" ftype="fasta" value="phiX.fa" /> 926 <param name="history_item" ftype="fasta" value="phiX.fa" />
904 <param name="input_1" ftype="fastqsanger.gz" value="hisat_input_1_interleaved.fastq.gz" /> 927 <param name="input_1" ftype="fastqsanger.gz" value="hisat_input_1_interleaved.fastq.gz" />
905 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> 928 <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >
929 <metadata name="sort_order" value="coordinate"/>
930 </output>
906 </test> 931 </test>
907 <!-- Ensure interleaved fasta input works --> 932 <!-- Ensure interleaved fasta input works -->
908 <test expect_num_outputs="1" > 933 <test expect_num_outputs="1" >
909 <param name="type" value="paired_interleaved" /> 934 <param name="type" value="paired_interleaved" />
910 <param name="source" value="history" /> 935 <param name="source" value="history" />
911 <param name="history_item" ftype="fasta" value="phiX.fa" /> 936 <param name="history_item" ftype="fasta" value="phiX.fa" />
912 <param name="input_1" ftype="fasta" value="hisat_input_1_interleaved.fasta" /> 937 <param name="input_1" ftype="fasta" value="hisat_input_1_interleaved.fasta" />
913 <output name="output_alignments" file="hisat_output_1_noqual.bam" ftype="bam" lines_diff="2" /> 938 <output name="output_alignments" file="hisat_output_1_noqual.bam" ftype="bam" lines_diff="2" sort="true" >
939 <metadata name="sort_order" value="coordinate"/>
940 </output>
914 </test> 941 </test>
915 <!-- Ensure novel splicesite file output works --> 942 <!-- Ensure novel splicesite file output works -->
916 <test> 943 <test>
917 <param name="type" value="single" /> 944 <param name="type" value="single" />
918 <param name="source" value="history" /> 945 <param name="source" value="history" />
919 <param name="history_item" ftype="fasta" value="phiX.fa" /> 946 <param name="history_item" ftype="fasta" value="phiX.fa" />
920 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_split_forward.fastq" /> 947 <param name="input_1" ftype="fastqsanger" value="hisat_input_1_split_forward.fastq" />
921 <param name="rna_strandness" value="R" /> 948 <param name="rna_strandness" value="R" />
922 <param name="adv|spliced_options|spliced_options_selector" value="advanced"/> 949 <param name="adv|spliced_options|spliced_options_selector" value="advanced"/>
923 <param name="adv|spliced_options|novel_splicesite_outfile" value="true" /> 950 <param name="adv|spliced_options|novel_splicesite_outfile" value="true" />
924 <output name="output_alignments" file="hisat_output_spliced_1.bam" ftype="bam" lines_diff="2" /> 951 <output name="output_alignments" file="hisat_output_spliced_1.bam" ftype="bam" lines_diff="2" sort="true" >
952 <metadata name="sort_order" value="coordinate"/>
953 </output>
925 <output name="novel_splicesite_output" file="novel_splicesite_out.tab" ftype="tabular" /> 954 <output name="novel_splicesite_output" file="novel_splicesite_out.tab" ftype="tabular" />
926 </test> 955 </test>
927 <!-- Ensure SAM output settings work --> 956 <!-- Ensure SAM output settings work -->
928 <test expect_num_outputs="1" > 957 <test expect_num_outputs="1" >
929 <param name="type" value="paired_interleaved" /> 958 <param name="type" value="paired_interleaved" />
939 <repeat name="adv|sam_options|read_groups|read_groups"> 968 <repeat name="adv|sam_options|read_groups|read_groups">
940 <param name="rg" value="CN:test2"/> 969 <param name="rg" value="CN:test2"/>
941 </repeat> 970 </repeat>
942 <param name="adv|sam_options|chr_text" value="--add-chrname"/> 971 <param name="adv|sam_options|chr_text" value="--add-chrname"/>
943 <param name="adv|sam_options|omit_sec_seq" value="True"/> 972 <param name="adv|sam_options|omit_sec_seq" value="True"/>
944 <output name="output_alignments" file="hisat_output_5.bam" ftype="bam" lines_diff="2" /> 973 <output name="output_alignments" file="hisat_output_5.bam" ftype="bam" lines_diff="2" sort="true" >
974 <metadata name="sort_order" value="coordinate"/>
975 </output>
945 </test> 976 </test>
946 </tests> 977 </tests>
947 978
948 <help><![CDATA[ 979 <help><![CDATA[
949 Introduction 980 Introduction