| Previous changeset 6:5f4da9ec47c7 (2016-11-09) Next changeset 8:4d0a3173cde0 (2017-02-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde |
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modified:
hisat2.xml hisat2_macros.xml tool_data_table_conf.xml.sample |
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added:
test-data/test_unaligned_reads.fasta |
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| diff -r 5f4da9ec47c7 -r 5ba8e317529a hisat2.xml --- a/hisat2.xml Wed Nov 09 05:57:35 2016 -0500 +++ b/hisat2.xml Sat Jan 21 15:42:34 2017 -0500 |
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| b'@@ -1,5 +1,5 @@\n <?xml version="1.0"?>\n-<tool id="hisat2" name="HISAT" version="2.0.3.1">\n+<tool id="hisat2" name="HISAT2" version="2.0.3.2">\n <description>A fast and sensitive alignment program</description>\n <macros>\n <import>hisat2_macros.xml</import>\n@@ -38,6 +38,12 @@\n @paired_end_options@\n #else:\n -U "${input_format.paired.reads}"\n+ #if str( $input_format.paired.unaligned_file ) == "true":\n+ --un \'$output_unaligned_reads_l\'\n+ #end if\n+ #if str( $input_format.paired.aligned_file ) == "true":\n+ --al \'$output_aligned_reads_l\'\n+ #end if\n #end if\n #if $input_format.input_format_selector == \'fasta\':\n -f\n@@ -84,6 +90,22 @@\n ${paired_options.dovetail} ${paired_options.contain} ${paired_options.overlap}\n #end if\n | samtools sort - -@ \\${GALAXY_SLOTS:-2} -l 6 -o hsbam > "${output_alignments}"\n+\n+ ## Rename any output fastq files\n+ #if str($input_format.paired.paired_selector) == \'paired\' or str($input_format.paired.paired_selector) == \'paired_collection\':\n+ #if $output_unaligned_reads_l and $output_unaligned_reads_r:\n+ #set left = str($output_unaligned_reads_l).replace(".dat", ".1.dat")\n+ #set right = str($output_unaligned_reads_l).replace(".dat", ".2.dat")\n+ && mv \'${left}\' \'${output_unaligned_reads_l}\'\n+ && mv \'${right}\' \'${output_unaligned_reads_r}\'\n+ #end if\n+ #if $output_aligned_reads_l and $output_aligned_reads_r:\n+ #set left = str($output_aligned_reads_l).replace(".dat", ".1.dat")\n+ #set right = str($output_aligned_reads_l).replace(".dat", ".2.dat")\n+ && mv \'${left}\' \'${output_aligned_reads_l}\'\n+ && mv \'${right}\' \'${output_aligned_reads_r}\'\n+ #end if\n+ #end if\n ]]>\n </command>\n <inputs>\n@@ -243,6 +265,84 @@\n </conditional>\n </actions>\n </data>\n+ <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >\n+ <filter>input_format[\'paired\'][\'unaligned_file\'] is True</filter>\n+ <actions>\n+ <conditional name="input_format.paired.paired_selector">\n+ <when value="single">\n+ <action type="format">\n+ <option type="from_param" name="input_format.paired.reads" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired">\n+ <action type="format">\n+ <option type="from_param" name="input_format.paired.reads_f" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired_collection">\n+ <action type="format">\n+ <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ </conditional>\n+ </actions>\n+ </data>\n+ <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)" >\n+ <filter>input_format[\'paired\'][\'unaligned_file\'] is True and input_format[\'paired\'][\'paired_selector\'] != \'single\'</filter>\n+ <actions>\n+ <conditional name="input_format.paired.paired_selector">\n+ <when value="paired">\n+ <action type="format">\n+ <option type="from_param" name="input_format.paired.reads_r" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired_collection">\n+ '..b' <actions>\n+ <conditional name="input_format.paired.paired_selector">\n+ <when value="single">\n+ <action type="format">\n+ <option type="from_param" name="input_format.paired.reads" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired">\n+ <action type="format">\n+ <option type="from_param" name="input_format.paired.reads_f" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired_collection">\n+ <action type="format">\n+ <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ </conditional>\n+ </actions>\n+ </data>\n+ <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)" >\n+ <filter>input_format[\'paired\'][\'aligned_file\'] is True and input_format[\'paired\'][\'paired_selector\'] != \'single\'</filter>\n+ <actions>\n+ <conditional name="input_format.paired.paired_selector">\n+ <when value="paired">\n+ <action type="format">\n+ <option type="from_param" name="input_format.paired.reads_r" param_attribute="ext" />\n+ </action>\n+ </when>\n+ <when value="paired_collection">\n+ <action type="format">\n+ <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" />\n+ </action>\n+ </when>\n+ </conditional>\n+ </actions>\n+ </data>\n </outputs>\n <tests>\n <test>\n@@ -281,6 +381,35 @@\n <param name="no_discordant" value="True" />\n <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" />\n </test>\n+ <test><!-- testing unaligned output (single dataset) -->\n+ <param name="input_format_selector" value="fasta" />\n+ <param name="paired_selector" value="single" />\n+ <param name="reference_genome_source" value="history" />\n+ <param name="history_item" value="phiX.fa" ftype="fasta" />\n+ <param name="unaligned_file" value="true" />\n+ <param name="aligned_file" value="true" />\n+ <param name="reference_genome_source" value="history" />\n+ <param name="history_item" value="phiX.fa" ftype="fasta" />\n+ <param name="reads" value="test_unaligned_reads.fasta" ftype="fasta" />\n+ \n+ <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />\n+ </test>\n+ \n+ <test>\n+ <param name="input_format_selector" value="fasta" />\n+ <param name="paired_selector" value="paired" />\n+ <param name="reference_genome_source" value="history" />\n+ <param name="history_item" value="phiX.fa" ftype="fasta" />\n+ <param name="unaligned_file" value="true" />\n+ <param name="aligned_file" value="true" />\n+ <param name="reference_genome_source" value="history" />\n+ <param name="history_item" value="phiX.fa" ftype="fasta" />\n+ <param name="reads_f" value="test_unaligned_reads.fasta" ftype="fasta" />\n+ <param name="reads_r" value="test_unaligned_reads.fasta" ftype="fasta" />\n+ \n+ <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" />\n+ <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" />\n+ </test>\n </tests>\n <help>\n <![CDATA[\n' |
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| diff -r 5f4da9ec47c7 -r 5ba8e317529a hisat2_macros.xml --- a/hisat2_macros.xml Wed Nov 09 05:57:35 2016 -0500 +++ b/hisat2_macros.xml Sat Jan 21 15:42:34 2017 -0500 |
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| @@ -23,14 +23,18 @@ <when value="paired_collection"> <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" /> <expand macro="paired_end_conditional" /> + <expand macro="paired_end_output" /> </when> <when value="paired"> <param format="@FTYPE@" label="Forward reads" name="reads_f" type="data" /> <param format="@FTYPE@" label="Reverse reads" name="reads_r" type="data" /> <expand macro="paired_end_conditional" /> + <expand macro="paired_end_output" /> </when> <when value="single"> <param format="@FTYPE@" label="Reads" name="reads" type="data" /> + <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un" /> + <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al" /> </when> </conditional> </xml> @@ -50,7 +54,17 @@ </when> </conditional> </xml> + <xml name="paired_end_output"> + <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un-conc" /> + <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al-conc" /> + </xml> <token name="@paired_end_options@"> + #if str( $input_format.paired.unaligned_file ) == "true": + --un-conc '${output_unaligned_reads_l}' + #end if + #if str( $input_format.paired.aligned_file ) == "true": + --al-conc '${output_aligned_reads_l}' + #end if #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced': ${input_format.paired.paired_end_options.no_mixed} ${input_format.paired.paired_end_options.no_discordant} |
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| diff -r 5f4da9ec47c7 -r 5ba8e317529a test-data/test_unaligned_reads.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_unaligned_reads.fasta Sat Jan 21 15:42:34 2017 -0500 |
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| @@ -0,0 +1,6 @@ +>read1 +aaaaaaaaaaaaaaaaaaaaaaaaaa +>read2 +aaaaaataaaaaaaaaaaaaaaaaaa +>read3 +aaaaaagaaaaaaaaaaaaaaaaaaa |
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| diff -r 5f4da9ec47c7 -r 5ba8e317529a tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Wed Nov 09 05:57:35 2016 -0500 +++ b/tool_data_table_conf.xml.sample Sat Jan 21 15:42:34 2017 -0500 |
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| @@ -1,6 +1,6 @@ <tables> <!-- Locations of indexes in the HISAT mapper format --> - <table name="hisat2_indexes" comment_char="#"> + <table name="hisat2_indexes" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> <file path="tool-data/hisat2_indexes.loc" /> </table> |