| Previous changeset 32:d5ceb9f3c25b (2024-05-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a |
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modified:
bowtie2_macros.xml bowtie2_wrapper.xml |
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added:
test-data/bowtie2-ref.1.bt2 test-data/bowtie2-ref.2.bt2 test-data/bowtie2-ref.3.bt2 test-data/bowtie2-ref.4.bt2 test-data/bowtie2-ref.rev.1.bt2 test-data/bowtie2-ref.rev.2.bt2 test-data/bowtie2-single.bam test-data/bowtie2_indices.loc tool_data_table_conf.xml.test |
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| diff -r d5ceb9f3c25b -r f76cbb84d67f bowtie2_macros.xml --- a/bowtie2_macros.xml Mon May 13 13:49:14 2024 +0000 +++ b/bowtie2_macros.xml Wed Sep 24 13:37:14 2025 +0000 |
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| @@ -1,6 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">2.5.3</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.5.4</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> <!-- Import this at the top of your command block and then define rg_auto_name. --> <token name="@define_read_group_helpers@"> @@ -59,7 +60,7 @@ #if $use_rg #if $rg_param('read_group_id_conditional') is None #set $rg_id = $rg_auto_name - #elif $rg_param('read_group_id_conditional').do_auto_name + #elif $rg_param('read_group_id_conditional').do_auto_name == "yes" #set $rg_id = $rg_auto_name #else #set $rg_id = str($rg_param('read_group_id_conditional').ID) @@ -67,7 +68,7 @@ #if $rg_param('read_group_sm_conditional') is None #set $rg_sm = '' - #elif $rg_param('read_group_sm_conditional').do_auto_name + #elif $rg_param('read_group_sm_conditional').do_auto_name == "yes" #set $rg_sm = $rg_auto_name #else #set $rg_sm = str($rg_param('read_group_sm_conditional').SM) @@ -81,7 +82,7 @@ #if $rg_param('read_group_lb_conditional') is None #set $rg_lb = '' - #elif $rg_param('read_group_lb_conditional').do_auto_name + #elif $rg_param('read_group_lb_conditional').do_auto_name == "yes" #set $rg_lb = $rg_auto_name #else #set $rg_lb = str($rg_param('read_group_lb_conditional').LB) @@ -140,15 +141,17 @@ #set $use_rg = str($rg.rg_selector) != "do_not_set" </token> <xml name="read_group_auto_name_conditional"> - <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="false" /> - <when value="true"> - </when> - <when value="false"> + <param name="do_auto_name" type="select" optional="false" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value"> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"/> + <when value="no"> <yield /> </when> </xml> <xml name="read_group_id_param"> - <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false"> + <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment"> <validator type="empty_field" /> </param> </xml> @@ -173,7 +176,7 @@ as per Picard. --> <xml name="read_group_sm_param_required"> - <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced"> + <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced"> <validator type="empty_field" /> </param> </xml> @@ -196,7 +199,7 @@ </param> </xml> <xml name="read_group_lb_param"> - <param name="LB" type="text" label="Library name (LB)" optional="true" /> + <param name="LB" type="text" label="Library name (LB)"/> </xml> <xml name="read_group_lb_conditional"> <conditional name="read_group_lb_conditional"> @@ -206,7 +209,7 @@ </conditional> </xml> <xml name="read_group_lb_required_param"> - <param name="LB" type="text" label="Library name (LB)" optional="false"> + <param name="LB" type="text" label="Library name (LB)"> <validator type="empty_field" /> </param> </xml> @@ -227,8 +230,8 @@ <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" /> </xml> <xml name="read_group_fo_param"> - <param name="FO" type="text" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/"> - <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator> + <param name="FO" type="text" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/"> + <validator type="regex" message="Invalid flow order">|\*|[ACMGRSVTWYHKDBN]+$</validator> </param> </xml> <xml name="read_group_ks_param"> @@ -241,10 +244,10 @@ <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" /> </xml> <xml name="read_group_pu_param"> - <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" /> + <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" /> </xml> <xml name="read_group_pu_required_param"> - <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> + <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" /> </xml> <!-- Only ID is required - all groups available --> <xml name="read_group_inputs_spec"> @@ -287,10 +290,8 @@ <when value="set"> <expand macro="read_group_inputs_spec" /> </when> - <when value="set_id_auto"> - </when> - <when value="do_not_set"> - </when> + <when value="set_id_auto"/> + <when value="do_not_set"/> </conditional> </xml> <xml name="paired_end_options"> |
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| diff -r d5ceb9f3c25b -r f76cbb84d67f bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Mon May 13 13:49:14 2024 +0000 +++ b/bowtie2_wrapper.xml Wed Sep 24 13:37:14 2025 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">\n+<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>- map reads against reference genome</description>\n <macros>\n <import>bowtie2_macros.xml</import>\n@@ -8,7 +8,7 @@\n </xrefs>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>\n- <requirement type="package" version="1.19.2">samtools</requirement>\n+ <requirement type="package" version="1.22.1">samtools</requirement>\n </requirements>\n <version_command>bowtie2 --version</version_command>\n <command detect_errors="exit_code"><![CDATA[\n@@ -28,34 +28,7 @@\n \n #set compressed="False"\n #set reads_are_fastq = True\n-#if str($library.type) == \'paired\':\n- #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set read1 = "input_f.fastq.gz"\n- #set compressed = "GZ"\n- #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read1 = "input_f.fastq.bz2"\n- #set compressed = "BZ2"\n- #else if $library.input_1.is_of_type(\'fasta\'):\n- #set reads_are_fastq = False\n- #set read1 = "input_f.fasta"\n- #else:\n- #set read1 = "input_f.fastq"\n- #end if\n- ln -f -s \'${library.input_1}\' ${read1} &&\n-\n- #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set read2 = "input_r.fastq.gz"\n- #set compressed = "GZ"\n- #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read2 = "input_r.fastq.bz2"\n- #set compressed = "BZ2"\n- #else if $library.input_2.is_of_type(\'fasta\'):\n- #set read2 = "input_r.fasta"\n- #else:\n- #set read2 = "input_r.fastq"\n- #end if\n- ln -f -s \'${library.input_2}\' ${read2} &&\n-#else if str($library.type) == \'paired_collection\':\n+#if str($library.type) == \'paired_collection\':\n #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):\n #set read1 = "input_f.fastq.gz"\n #set compressed = "GZ"\n@@ -82,21 +55,6 @@\n #set read2 = "input_r.fastq"\n #end if\n ln -f -s \'${library.input_1.reverse}\' ${read2} &&\n-\n-#else if str($library.type) == \'paired_interleaved\':\n- #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set read1 = "input_il.fastq.gz"\n- #set compressed = "GZ"\n- #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set read1 = "input_il.fastq.bz2"\n- #set compressed = "BZ2"\n- #else if $library.input_1.is_of_type("fasta"):\n- #set reads_are_fastq = False\n- #set read1 = "input_il.fasta"\n- #else:\n- #set read1 = "input_il.fastq"\n- #end if\n- ln -f -s \'${library.input_1}\' ${read1} &&\n #else:\n #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):\n #set read1 = "input_f.fastq.gz"\n@@ -143,62 +101,42 @@\n -U \'${read1}\'\n #if str( $library.unaligned_file ) == "true":\n #if $compressed == "GZ":\n- --un-gz \'${output_unaligned_reads_l}\'\n+ --un-gz \'unaligned_reads\'\n #else if $compressed == "BZ2":\n- --un-bz2 \'${output_unaligned_reads_l}\'\n+ --un-bz2 \'unaligned_reads\'\n #else:\n- --un \'${output_unaligned_reads_l}\'\n+ --un \'unaligned_reads\'\n #end if\n #end if\n #if str( $library.aligned_file ) == "true":\n #if $compressed == "GZ":\n- --al-gz \'${output_aligned_reads_l}\'\n+ --al-gz \'aligned_reads\'\n #else if $compressed == "BZ2":\n- --al-bz2 \'${output_aligned_reads_l}\'\n+ --al-bz2 \'aligned_reads\'\n #else:\n- --al \'${output_aligned_reads_l}\'\n+ --al \'aligned_reads\'\n #end if\n #end if\n \n-#elif str( $library.type ) == "paired_interleaved":\n- --interleaved \'${read1}\'\n- #if str( $library.unaligned_'..b'history" />\n- <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>\n- <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>\n- <param name="own_file" value="bowtie2-ref.fasta" />\n- <param name="sam_options_selector" value="yes" />\n- <param name="reorder" value="true" />\n+ <conditional name="library">\n+ <param name="type" value="paired_collection"/>\n+ <conditional name="paired_options">\n+ <param name="paired_options_selector" value="no"/>\n+ </conditional>\n+ <param name="unaligned_file" value="false"/>\n+ <param name="input_1">\n+ <collection type="paired">\n+ <element name="forward" value="bowtie2-fq1.fa" ftype="fasta" />\n+ <element name="reverse" value="bowtie2-fq2.fa" ftype="fasta" />\n+ </collection>\n+ </param>\n+ </conditional>\n+ <conditional name="analysis_type">\n+ <param name="analysis_type_selector" value="simple"/>\n+ </conditional>\n+ <conditional name="reference_genome">\n+ <param name="source" value="history" />\n+ <param name="own_file" value="bowtie2-ref.fasta" />\n+ </conditional>\n+ <conditional name="sam_options">\n+ <param name="sam_options_selector" value="yes" />\n+ <param name="reorder" value="true" />\n+ </conditional>\n <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" lines_diff="4">\n <metadata name="sort_order" value="unsorted"/>\n </output>\n </test>\n+ <!-- test on fasta paired-end datasets with sam as output -->\n <test expect_num_outputs="1">\n- <!-- test on fasta paired-end datasets with sam as output -->\n- <param name="type" value="paired"/>\n- <param name="paired_options_selector" value="no"/>\n- <param name="unaligned_file" value="false"/>\n- <param name="analysis_type_selector" value="simple"/>\n- <param name="source" value="history" />\n- <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>\n- <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>\n- <param name="own_file" value="bowtie2-ref.fasta" />\n- <param name="sam_options_selector" value="yes" />\n- <param name="sam_options|sam_opt" value="true" />\n+ <conditional name="library">\n+ <param name="type" value="paired_collection"/>\n+ <conditional name="paired_options">\n+ <param name="paired_options_selector" value="no"/>\n+ </conditional>\n+ <param name="unaligned_file" value="false"/>\n+ <param name="input_1">\n+ <collection type="paired">\n+ <element name="forward" value="bowtie2-fq1.fa" ftype="fasta" />\n+ <element name="reverse" value="bowtie2-fq2.fa" ftype="fasta" />\n+ </collection>\n+ </param>\n+ </conditional>\n+ <conditional name="analysis_type">\n+ <param name="analysis_type_selector" value="simple"/>\n+ </conditional>\n+ <conditional name="reference_genome">\n+ <param name="source" value="history" />\n+ <param name="own_file" value="bowtie2-ref.fasta" />\n+ </conditional>\n+ <conditional name="sam_options">\n+ <param name="sam_options_selector" value="yes" />\n+ <param name="sam_opt" value="true" />\n+ </conditional>\n <output name="output" ftype="sam">\n <metadata name="sort_order" value="unsorted"/>\n <assert_contents>\n' |
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| diff -r d5ceb9f3c25b -r f76cbb84d67f test-data/bowtie2_indices.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie2_indices.loc Wed Sep 24 13:37:14 2025 +0000 |
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| @@ -0,0 +1,38 @@ +# bowtie2_indices.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a bowtie_indices.loc file to use those indexes with tools. +# Copy this file, save it with the same name (minus the .sample), +# follow the format examples, and store the result in this directory. +# The file should include an one line entry for each index set. +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +# So, for example, if you had hg18 indexes stored in: +# +# /depot/data2/galaxy/hg19/bowtie2/ +# +# containing hg19 genome and hg19.*.bt2 files, such as: +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 +# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 +# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 +# +# then the bowtie2_indices.loc entry could look like this: +# +#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 +# +# +test_value test_dbkey test_name ${__HERE__}/bowtie2-ref \ No newline at end of file |
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| diff -r d5ceb9f3c25b -r f76cbb84d67f tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Sep 24 13:37:14 2025 +0000 |
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| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the Bowtie2 mapper format --> + <table name="bowtie2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/bowtie2_indices.loc" /> + </table> +</tables> |