| Previous changeset 30:6c19daec423d (2021-07-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03 |
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modified:
hisat2.xml hisat2_macros.xml |
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| diff -r 6c19daec423d -r f4af63aaf57a hisat2.xml --- a/hisat2.xml Sun Jul 18 17:50:55 2021 +0000 +++ b/hisat2.xml Wed Jul 06 10:26:44 2022 +0000 |
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| b'@@ -3,6 +3,9 @@\n <macros>\n <import>hisat2_macros.xml</import>\n </macros>\n+ <xrefs>\n+ <xref type="bio.tools">hisat2</xref>\n+ </xrefs>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">hisat2</requirement>\n <requirement type="package" version="1.12">samtools</requirement>\n@@ -561,8 +564,8 @@\n <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"/>\n <conditional name="read_groups">\n <param name="rg_labels" type="select" label="Edit Read Group IDs">\n- <option value="No" />\n- <option value="Yes" />\n+ <option value="No">No</option>\n+ <option value="Yes">Yes</option>\n </param>\n <when value="No"/>\n <when value="Yes">\n@@ -758,7 +761,9 @@\n <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />\n <param name="adv|reporting_options|reporting_options_selector" value="advanced"/>\n <param name="novel_splicesite_outfile" value="false" />\n- <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />\n+ <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" >\n+ <metadata name="sort_order" value="coordinate"/>\n+ </output>\n </test>\n <!-- Ensure advanced scoring options work -->\n <test expect_num_outputs="1" >\n@@ -768,7 +773,9 @@\n <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />\n <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />\n <param name="adv|scoring_options|coefficient" value="-0.3"/>\n- <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />\n+ <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >\n+ <metadata name="sort_order" value="coordinate"/>\n+ </output>\n </test>\n <!-- Ensure built-in reference works -->\n <test expect_num_outputs="1">\n@@ -776,7 +783,9 @@\n <param name="source" value="indexed" />\n <param name="input_1" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_forward.fastq" />\n <param name="input_2" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_reverse.fastq" />\n- <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />\n+ <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >\n+ <metadata name="sort_order" value="coordinate"/>\n+ </output>\n </test>\n <!-- Ensure trimming works -->\n <test expect_num_outputs="1">\n@@ -788,7 +797,9 @@\n <param name="trim5" value="15" />\n <param name="input_1" ftype="fastqsanger" value="hisat_input_2_forward.fastq" />\n <param name="input_2" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />\n- <output name="output_alignments" file="hisat_output_2.bam" ftype="bam" lines_diff="2" />\n+ <output name="output_alignments" file="hisat_output_2.bam" ftype="bam" lines_diff="2" sort="true" >\n+ <metadata name="sort_order" value="coordinate"/>\n+ </output>\n </test>\n <!-- Ensure paired options works -->\n <test expect_num_outputs="1">\n@@ -803,7 +814,9 @@\n <param name="paired_options_selector" value="advanced" />\n <param name="no_mixed" value="True" />\n <param name="no_discordant" value="True" />\n- '..b' output works -->\n <test expect_num_outputs="2">\n@@ -886,7 +905,9 @@\n <param name="source" value="history" />\n <param name="history_item" ftype="fasta" value="phiX.fa" />\n <param name="input_1" ftype="fastqsanger" value="hisat_input_1_interleaved.fastq" />\n- <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />\n+ <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >\n+ <metadata name="sort_order" value="coordinate"/>\n+ </output>\n </test>\n <!-- Ensure interleaved bz input works -->\n <test expect_num_outputs="1" >\n@@ -894,7 +915,9 @@\n <param name="source" value="history" />\n <param name="history_item" ftype="fasta" value="phiX.fa" />\n <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_1_interleaved.fastq.bz2" />\n- <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />\n+ <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >\n+ <metadata name="sort_order" value="coordinate"/>\n+ </output>\n </test>\n <!-- Ensure interleaved gz input works -->\n <test expect_num_outputs="1" >\n@@ -902,7 +925,9 @@\n <param name="source" value="history" />\n <param name="history_item" ftype="fasta" value="phiX.fa" />\n <param name="input_1" ftype="fastqsanger.gz" value="hisat_input_1_interleaved.fastq.gz" />\n- <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />\n+ <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >\n+ <metadata name="sort_order" value="coordinate"/>\n+ </output>\n </test>\n <!-- Ensure interleaved fasta input works -->\n <test expect_num_outputs="1" >\n@@ -910,7 +935,9 @@\n <param name="source" value="history" />\n <param name="history_item" ftype="fasta" value="phiX.fa" />\n <param name="input_1" ftype="fasta" value="hisat_input_1_interleaved.fasta" />\n- <output name="output_alignments" file="hisat_output_1_noqual.bam" ftype="bam" lines_diff="2" />\n+ <output name="output_alignments" file="hisat_output_1_noqual.bam" ftype="bam" lines_diff="2" sort="true" >\n+ <metadata name="sort_order" value="coordinate"/>\n+ </output>\n </test>\n <!-- Ensure novel splicesite file output works -->\n <test>\n@@ -921,7 +948,9 @@\n <param name="rna_strandness" value="R" />\n <param name="adv|spliced_options|spliced_options_selector" value="advanced"/>\n <param name="adv|spliced_options|novel_splicesite_outfile" value="true" />\n- <output name="output_alignments" file="hisat_output_spliced_1.bam" ftype="bam" lines_diff="2" />\n+ <output name="output_alignments" file="hisat_output_spliced_1.bam" ftype="bam" lines_diff="2" sort="true" >\n+ <metadata name="sort_order" value="coordinate"/>\n+ </output>\n <output name="novel_splicesite_output" file="novel_splicesite_out.tab" ftype="tabular" />\n </test>\n <!-- Ensure SAM output settings work -->\n@@ -941,7 +970,9 @@\n </repeat> \n <param name="adv|sam_options|chr_text" value="--add-chrname"/>\n <param name="adv|sam_options|omit_sec_seq" value="True"/> \n- <output name="output_alignments" file="hisat_output_5.bam" ftype="bam" lines_diff="2" />\n+ <output name="output_alignments" file="hisat_output_5.bam" ftype="bam" lines_diff="2" sort="true" >\n+ <metadata name="sort_order" value="coordinate"/>\n+ </output>\n </test>\n </tests>\n \n' |
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| diff -r 6c19daec423d -r f4af63aaf57a hisat2_macros.xml --- a/hisat2_macros.xml Sun Jul 18 17:50:55 2021 +0000 +++ b/hisat2_macros.xml Wed Jul 06 10:26:44 2022 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.2.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="paired_end_options"> |