Mercurial > repos > devteam > bowtie2
changeset 33:f76cbb84d67f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 4508a3878ac8d12306a7521aa55fa286710d947a
| author | iuc |
|---|---|
| date | Wed, 24 Sep 2025 13:37:14 +0000 |
| parents | d5ceb9f3c25b |
| children | |
| files | bowtie2_macros.xml bowtie2_wrapper.xml 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 |
| diffstat | 11 files changed, 422 insertions(+), 318 deletions(-) [+] |
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--- a/bowtie2_macros.xml Mon May 13 13:49:14 2024 +0000 +++ b/bowtie2_macros.xml Wed Sep 24 13:37:14 2025 +0000 @@ -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">
--- a/bowtie2_wrapper.xml Mon May 13 13:49:14 2024 +0000 +++ b/bowtie2_wrapper.xml Wed Sep 24 13:37:14 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> +<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>- map reads against reference genome</description> <macros> <import>bowtie2_macros.xml</import> @@ -8,7 +8,7 @@ </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement> - <requirement type="package" version="1.19.2">samtools</requirement> + <requirement type="package" version="1.22.1">samtools</requirement> </requirements> <version_command>bowtie2 --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -28,34 +28,7 @@ #set compressed="False" #set reads_are_fastq = True -#if str($library.type) == 'paired': - #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): - #set read1 = "input_f.fastq.gz" - #set compressed = "GZ" - #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set read1 = "input_f.fastq.bz2" - #set compressed = "BZ2" - #else if $library.input_1.is_of_type('fasta'): - #set reads_are_fastq = False - #set read1 = "input_f.fasta" - #else: - #set read1 = "input_f.fastq" - #end if - ln -f -s '${library.input_1}' ${read1} && - - #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"): - #set read2 = "input_r.fastq.gz" - #set compressed = "GZ" - #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set read2 = "input_r.fastq.bz2" - #set compressed = "BZ2" - #else if $library.input_2.is_of_type('fasta'): - #set read2 = "input_r.fasta" - #else: - #set read2 = "input_r.fastq" - #end if - ln -f -s '${library.input_2}' ${read2} && -#else if str($library.type) == 'paired_collection': +#if str($library.type) == 'paired_collection': #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): #set read1 = "input_f.fastq.gz" #set compressed = "GZ" @@ -82,21 +55,6 @@ #set read2 = "input_r.fastq" #end if ln -f -s '${library.input_1.reverse}' ${read2} && - -#else if str($library.type) == 'paired_interleaved': - #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): - #set read1 = "input_il.fastq.gz" - #set compressed = "GZ" - #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): - #set read1 = "input_il.fastq.bz2" - #set compressed = "BZ2" - #else if $library.input_1.is_of_type("fasta"): - #set reads_are_fastq = False - #set read1 = "input_il.fasta" - #else: - #set read1 = "input_il.fastq" - #end if - ln -f -s '${library.input_1}' ${read1} && #else: #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): #set read1 = "input_f.fastq.gz" @@ -143,62 +101,42 @@ -U '${read1}' #if str( $library.unaligned_file ) == "true": #if $compressed == "GZ": - --un-gz '${output_unaligned_reads_l}' + --un-gz 'unaligned_reads' #else if $compressed == "BZ2": - --un-bz2 '${output_unaligned_reads_l}' + --un-bz2 'unaligned_reads' #else: - --un '${output_unaligned_reads_l}' + --un 'unaligned_reads' #end if #end if #if str( $library.aligned_file ) == "true": #if $compressed == "GZ": - --al-gz '${output_aligned_reads_l}' + --al-gz 'aligned_reads' #else if $compressed == "BZ2": - --al-bz2 '${output_aligned_reads_l}' + --al-bz2 'aligned_reads' #else: - --al '${output_aligned_reads_l}' + --al 'aligned_reads' #end if #end if -#elif str( $library.type ) == "paired_interleaved": - --interleaved '${read1}' - #if str( $library.unaligned_file ) == "true": - #if $compressed == "GZ": - --un-gz '${output_unaligned_reads_l}' - #else if $compressed == "BZ2": - --un-bz2 '${output_unaligned_reads_l}' - #else: - --un '${output_unaligned_reads_l}' - #end if - #end if - #if str( $library.aligned_file ) == "true": - #if $compressed == "GZ": - --al-gz '${output_aligned_reads_l}' - #else if $compressed == "BZ2": - --al-bz2 '${output_aligned_reads_l}' - #else: - --al '${output_aligned_reads_l}' - #end if - #end if #else: -1 '${read1}' -2 '${read2}' #if str( $library.unaligned_file ) == "true": #if $compressed == "GZ": - --un-conc-gz '${output_unaligned_reads_l}' + --un-conc-gz 'unaligned_reads' #else if $compressed == "BZ2": - --un-conc-bz2 '${output_unaligned_reads_l}' + --un-conc-bz2 'unaligned_reads' #else: - --un-conc '${output_unaligned_reads_l}' + --un-conc 'unaligned_reads' #end if #end if #if str( $library.aligned_file ) == "true": #if $compressed == "GZ": - --al-conc-gz '${output_aligned_reads_l}' + --al-conc-gz 'aligned_reads' #else if $compressed == "BZ2": - --al-conc-bz2 '${output_aligned_reads_l}' + --al-conc-bz2 'aligned_reads' #else: - --al-conc '${output_aligned_reads_l}' + --al-conc 'aligned_reads' #end if #end if #if str( $library.paired_options.paired_options_selector ) == "yes": @@ -217,8 +155,6 @@ @define_read_group_helpers@ #if str( $library.type ) == "single": #set $rg_auto_name = $read_group_name_default($library.input_1) -#elif str( $library.type ) == "paired": - #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2) #else #set $rg_auto_name = $read_group_name_default($library.input_1) #end if @@ -333,51 +269,23 @@ #else: > '$output' #end if - -## rename unaligned sequence files -#if ($library.type == "paired" or $library.type == "paired_collection") and $output_unaligned_reads_l and $output_unaligned_reads_r: - #from os.path import splitext - #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) ) - && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l' - && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r' -#end if -#if ($library.type == "paired" or $library.type == "paired_collection") and $output_aligned_reads_l and $output_aligned_reads_r: - #from os.path import splitext - #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) ) - && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l' - && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r' -#end if - ]]></command> <inputs> <!-- single/paired --> <conditional name="library"> <param name="type" type="select" label="Is this single or paired library"> <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - <option value="paired_collection">Paired-end Dataset Collection</option> - <option value="paired_interleaved">Paired-end data from single interleaved dataset</option> + <option value="paired_collection">Paired-end</option> </param> <when value="single"> <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype "fastqsanger" or "fasta"" /> <expand macro="align_unalign" /> </when> - <when value="paired"> - <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype "fastqsanger"or "fasta"" /> - <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype "fastqsanger"or "fasta"" /> - <expand macro="align_unalign" /> - <expand macro="paired_end_options" /> - </when> <when value="paired_collection"> <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger" or "fasta"" /> <expand macro="align_unalign" /> <expand macro="paired_end_options" /> </when> - <when value="paired_interleaved"> - <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype "fastqsanger" or "fasta". --interleaved"/> - <expand macro="align_unalign" /> - <expand macro="paired_end_options" /> - </when> </conditional> <!-- reference genome --> <conditional name="reference_genome"> @@ -556,89 +464,47 @@ </inputs> <!-- define outputs --> <outputs> - <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > - <filter>library['unaligned_file'] is True</filter> + <data name="output_unaligned_reads" format_source="library|input_1" from_work_dir="unaligned_reads" label="${tool.name} on ${on_string}: unaligned reads" > + <filter>library['type'] == 'single' and library['unaligned_file'] is True</filter> <actions> - <conditional name="library.type"> - <when value="single"> - <action type="format"> - <option type="from_param" name="library.input_1" param_attribute="ext" /> - </action> - </when> - <when value="paired"> - <action type="format"> - <option type="from_param" name="library.input_1" param_attribute="ext" /> - </action> - </when> - <when value="paired_collection"> - <action type="format"> - <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> - </action> - </when> - </conditional> <expand macro="dbKeyActions" /> </actions> </data> - <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" > - <filter>library['aligned_file'] is True</filter> + <collection name="output_unaligned_read_pairs" type="paired" label="${tool.name} on ${on_string}: unaligned read pairs"> + <filter>library['type'] != 'single' and library['unaligned_file'] is True</filter> + <data name="forward" from_work_dir="unaligned_reads.1" format_source="library|input_1['forward']"> + <actions> + <expand macro="dbKeyActions" /> + </actions> + </data> + <data name="reverse" from_work_dir="unaligned_reads.2" format_source="library|input_1['reverse']"> + <actions> + <expand macro="dbKeyActions" /> + </actions> + </data> + </collection> + + <data name="output_aligned_reads" format_source="library|input_1" from_work_dir="aligned_reads" label="${tool.name} on ${on_string}: aligned reads" > + <filter>library['type'] == 'single' and library['aligned_file'] is True</filter> <actions> - <conditional name="library.type"> - <when value="single"> - <action type="format"> - <option type="from_param" name="library.input_1" param_attribute="ext" /> - </action> - </when> - <when value="paired"> - <action type="format"> - <option type="from_param" name="library.input_1" param_attribute="ext" /> - </action> - </when> - <when value="paired_collection"> - <action type="format"> - <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> - </action> - </when> - </conditional> <expand macro="dbKeyActions" /> </actions> </data> - <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)"> - <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter> - <actions> - <conditional name="library.type"> - <when value="paired"> - <action type="format"> - <option type="from_param" name="library.input_2" param_attribute="ext" /> - </action> - </when> - <when value="paired_collection"> - <action type="format"> - <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> - </action> - </when> - </conditional> - <expand macro="dbKeyActions" /> - </actions> - </data> - <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> - <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter> - <actions> - <conditional name="library.type"> - <when value="paired"> - <action type="format"> - <option type="from_param" name="library.input_2" param_attribute="ext" /> - </action> - </when> - <when value="paired_collection"> - <action type="format"> - <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> - </action> - </when> - </conditional> - <expand macro="dbKeyActions" /> - </actions> - </data> - <data format="bam" name="output" label="${tool.name} on ${on_string}: alignments"> + <collection name="output_aligned_read_pairs" type="paired" label="${tool.name} on ${on_string}: aligned read pairs"> + <filter>library['type'] != 'single' and library['aligned_file'] is True</filter> + <data name="forward" from_work_dir="aligned_reads.1" format_source="library|input_1['forward']"> + <actions> + <expand macro="dbKeyActions" /> + </actions> + </data> + <data name="reverse" from_work_dir="aligned_reads.2" format_source="library|input_1['forward']"> + <actions> + <expand macro="dbKeyActions" /> + </actions> + </data> + </collection> + + <data name="output" format="bam" label="${tool.name} on ${on_string}: alignments"> <change_format> <when input="sam_options.reorder" value="--reorder" format="qname_input_sorted.bam" /> <when input="sam_options.sam_opt" value="true" format="sam" /> @@ -670,65 +536,157 @@ </data> </outputs> <tests> + <!-- test on single-end datasets --> + <test expect_num_outputs="2"> + <conditional name="library"> + <param name="type" value="single"/> + <param name="unaligned_file" value="true"/> + <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger" /> + </conditional> + <conditional name="reference_genome"> + <param name="source" value="history" /> + <param name="own_file" value="bowtie2-ref.fasta" /> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="simple"/> + </conditional> + <output name="output_unaligned_reads" ftype="fastqsanger"> + <assert_contents> + <has_n_lines n="312"/> + </assert_contents> + </output> + <output name="output" file="bowtie2-single.bam" ftype="bam" lines_diff="4" sort="true"> + <metadata name="sort_order" value="coordinate"/> + </output> + </test> + <!-- test on paired-end datasets --> <test expect_num_outputs="1"> - <!-- test on paired-end datasets --> - <param name="type" value="paired"/> - <param name="paired_options_selector" value="no"/> - <param name="unaligned_file" value="false"/> - <param name="analysis_type_selector" value="simple"/> - <param name="source" value="history" /> - <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> - <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> - <param name="own_file" value="bowtie2-ref.fasta" /> + <conditional name="library"> + <param name="type" value="paired_collection"/> + <conditional name="paired_options"> + <param name="paired_options_selector" value="no"/> + </conditional> + <param name="unaligned_file" value="false"/> + <param name="input_1"> + <collection type="paired"> + <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> + <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> + </collection> + </param> + </conditional> + <conditional name="reference_genome"> + <param name="source" value="history" /> + <param name="own_file" value="bowtie2-ref.fasta" /> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="simple"/> + </conditional> <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true"> <metadata name="sort_order" value="coordinate"/> </output> </test> - <test expect_num_outputs="3"> - <!-- test on list paired collection --> - <param name="type" value="paired_collection"/> - <param name="paired_options_selector" value="no"/> - <param name="unaligned_file" value="true"/> - <param name="analysis_type_selector" value="simple"/> - <param name="source" value="history" /> - <param name="input_1"> - <collection type="paired"> - <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> - <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> - </collection> - </param> - <param name="own_file" value="bowtie2-ref.fasta" /> + <!-- test on paired-end datasets + unaligned output --> + <test expect_num_outputs="4"> + <conditional name="library"> + <param name="type" value="paired_collection"/> + <conditional name="paired_options"> + <param name="paired_options_selector" value="no"/> + </conditional> + <param name="unaligned_file" value="true"/> + <param name="input_1"> + <collection type="paired"> + <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> + <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> + </collection> + </param> + </conditional> + <conditional name="reference_genome"> + <param name="source" value="history" /> + <param name="own_file" value="bowtie2-ref.fasta" /> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="simple"/> + </conditional> + <output_collection name="output_unaligned_read_pairs" type="paired"> + <element name="forward" ftype="fastqsanger"> + <assert_contents> + <has_n_lines n="388"/> + </assert_contents> + </element> + <element name="reverse" ftype="fastqsanger"> + <assert_contents> + <has_n_lines n="388"/> + </assert_contents> + </element> + </output_collection> <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true"> <metadata name="sort_order" value="coordinate"/> </output> </test> <test expect_num_outputs="1"> <!-- test on paired-end datasets with read group info --> - <param name="type" value="paired"/> - <param name="paired_options_selector" value="no"/> - <param name="unaligned_file" value="false"/> - <param name="analysis_type_selector" value="simple"/> - <param name="rg_selector" value="set"/> - <param name="ID" value="rg1"/> - <param name="PL" value="CAPILLARY"/> - <param name="source" value="history" /> - <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> - <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> - <param name="own_file" value="bowtie2-ref.fasta" /> - <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="4" sort="true"> - <metadata name="sort_order" value="coordinate"/> + <conditional name="library"> + <param name="type" value="paired_collection"/> + <conditional name="paired_options"> + <param name="paired_options_selector" value="no"/> + </conditional> + <param name="unaligned_file" value="false"/> + <param name="input_1"> + <collection type="paired"> + <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> + <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> + </collection> + </param> + </conditional> + <conditional name="reference_genome"> + <param name="source" value="history" /> + <param name="own_file" value="bowtie2-ref.fasta" /> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="simple"/> + </conditional> + <conditional name="sam_options"> + <param name="sam_options_selector" value="yes" /> + <param name="sam_opt" value="true" /> + </conditional> + <conditional name="rg"> + <param name="rg_selector" value="set"/> + <conditional name="read_group_id_conditional"> + <param name="do_auto_name" value="no"/> + <param name="ID" value="rg1"/> + </conditional> + <param name="PL" value="CAPILLARY"/> + </conditional> + <output name="output" ftype="sam" lines_diff="4" sort="true"> + <metadata name="sort_order" value="unsorted"/> + <assert_contents> + <has_line line="@RG	ID:rg1	PL:CAPILLARY"/> + <has_text text="RG:Z:rg1" n="200"/> + </assert_contents> </output> </test> + <!-- test on paired-end datasets with stats output --> <test expect_num_outputs="2"> - <!-- test on paired-end datasets with stats output --> - <param name="type" value="paired"/> - <param name="paired_options_selector" value="no"/> - <param name="unaligned_file" value="false"/> - <param name="analysis_type_selector" value="simple"/> - <param name="source" value="history" /> - <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> - <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> - <param name="own_file" value="bowtie2-ref.fasta" /> + <conditional name="library"> + <param name="type" value="paired_collection"/> + <conditional name="paired_options"> + <param name="paired_options_selector" value="no"/> + </conditional> + <param name="unaligned_file" value="false"/> + <param name="input_1"> + <collection type="paired"> + <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" /> + <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" /> + </collection> + </param> + </conditional> + <conditional name="reference_genome"> + <param name="source" value="history" /> + <param name="own_file" value="bowtie2-ref.fasta" /> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="simple"/> + </conditional> <param name="save_mapping_stats" value="true" /> <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true"> <metadata name="sort_order" value="coordinate"/> @@ -739,92 +697,191 @@ </assert_contents> </output> </test> - <test expect_num_outputs="1"> - <!-- test on interleaved dataset --> - <param name="type" value="paired_interleaved"/> - <!-- <param name="paired_options_selector" value="no"/> --> - <param name="unaligned_file" value="false"/> - <param name="analysis_type_selector" value="simple"/> - <param name="rg_selector" value="set"/> - <param name="ID" value="rg1"/> - <param name="PL" value="CAPILLARY"/> - <param name="source" value="history" /> - <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/> - <param name="own_file" value="bowtie2-ref.fasta" /> - <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="4" sort="true"> + <!-- test on fastqsanger.gz paired-end datasets plus reference from data table --> + <test expect_num_outputs="4"> + <conditional name="library"> + <param name="type" value="paired_collection"/> + <conditional name="paired_options"> + <param name="paired_options_selector" value="no"/> + </conditional> + <param name="unaligned_file" value="true"/> + <param name="input_1"> + <collection type="paired"> + <element name="forward" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz" /> + <element name="reverse" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz" /> + </collection> + </param> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="simple"/> + </conditional> + <conditional name="reference_genome"> + <param name="source" value="indexed" /> + <param name="index" value="test_value" /> + </conditional> + <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true"> <metadata name="sort_order" value="coordinate"/> </output> + <output_collection name="output_unaligned_read_pairs" type="paired"> + <element name="forward" ftype="fastqsanger.gz" decompress="true"> + <assert_contents> + <has_n_lines n="388"/> + </assert_contents> + </element> + <element name="reverse" ftype="fastqsanger.gz" decompress="true"> + <assert_contents> + <has_n_lines n="388"/> + </assert_contents> + </element> + </output_collection> </test> - <test expect_num_outputs="1"> - <!-- test on fastqsanger.gz paired-end datasets --> - <param name="type" value="paired"/> - <param name="paired_options_selector" value="no"/> - <param name="unaligned_file" value="false"/> - <param name="analysis_type_selector" value="simple"/> - <param name="source" value="history" /> - <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/> - <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/> - <param name="own_file" value="bowtie2-ref.fasta" /> + <!-- test on fastqsanger.bz2 paired-end datasets --> + <test expect_num_outputs="4"> + <conditional name="library"> + <param name="type" value="paired_collection"/> + <conditional name="paired_options"> + <param name="paired_options_selector" value="no"/> + </conditional> + <param name="aligned_file" value="true"/> + <param name="input_1"> + <collection type="paired"> + <element name="forward" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2" /> + <element name="reverse" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2" /> + </collection> + </param> + </conditional> + <conditional name="reference_genome"> + <param name="source" value="history" /> + <param name="own_file" value="bowtie2-ref.fasta" /> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="simple"/> + </conditional> <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true"> <metadata name="sort_order" value="coordinate"/> </output> + <output_collection name="output_aligned_read_pairs" type="paired"> + <element name="forward" ftype="fastqsanger.bz2" decompress="true"> + <assert_contents> + <has_n_lines n="12"/> + </assert_contents> + </element> + <element name="reverse" ftype="fastqsanger.bz2" decompress="true"> + <assert_contents> + <has_n_lines n="12"/> + </assert_contents> + </element> + </output_collection> </test> - <test expect_num_outputs="1"> - <!-- test on fastqsanger.bz2 paired-end datasets --> - <param name="type" value="paired"/> - <param name="paired_options_selector" value="no"/> - <param name="unaligned_file" value="false"/> - <param name="analysis_type_selector" value="simple"/> - <param name="source" value="history" /> - <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/> - <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/> - <param name="own_file" value="bowtie2-ref.fasta" /> - <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true"> - <metadata name="sort_order" value="coordinate"/> - </output> - </test> - <test expect_num_outputs="1"> - <!-- test on fasta paired-end datasets --> - <param name="type" value="paired"/> - <param name="paired_options_selector" value="no"/> - <param name="unaligned_file" value="false"/> - <param name="analysis_type_selector" value="simple"/> - <param name="source" value="history" /> - <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> - <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> - <param name="own_file" value="bowtie2-ref.fasta" /> + <!-- test on fasta paired-end datasets + aligned + unaligned --> + <test expect_num_outputs="7"> + <conditional name="library"> + <param name="type" value="paired_collection"/> + <conditional name="paired_options"> + <param name="paired_options_selector" value="no"/> + </conditional> + <param name="unaligned_file" value="true"/> + <param name="aligned_file" value="true"/> + <param name="input_1"> + <collection type="paired"> + <element name="forward" value="bowtie2-fq1.fa" ftype="fasta" /> + <element name="reverse" value="bowtie2-fq2.fa" ftype="fasta" /> + </collection> + </param> + </conditional> + <conditional name="reference_genome"> + <param name="source" value="history" /> + <param name="own_file" value="bowtie2-ref.fasta" /> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="simple"/> + </conditional> + + <output_collection name="output_unaligned_read_pairs" type="paired"> + <element name="forward" ftype="fasta" decompress="true"> + <assert_contents> + <has_n_lines n="194"/> + </assert_contents> + </element> + <element name="reverse" ftype="fasta" decompress="true"> + <assert_contents> + <has_n_lines n="194"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="output_aligned_read_pairs" type="paired"> + <element name="forward" ftype="fasta" decompress="true"> + <assert_contents> + <has_n_lines n="6"/> + </assert_contents> + </element> + <element name="reverse" ftype="fasta" decompress="true"> + <assert_contents> + <has_n_lines n="6"/> + </assert_contents> + </element> + </output_collection> + <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4" sort="true"> <metadata name="sort_order" value="coordinate"/> </output> </test> + <!-- test on fasta paired-end datasets with bam_native as output --> <test expect_num_outputs="1"> - <!-- test on fasta paired-end datasets with bam_native as output --> - <param name="type" value="paired"/> - <param name="paired_options_selector" value="no"/> - <param name="unaligned_file" value="false"/> - <param name="analysis_type_selector" value="simple"/> - <param name="source" value="history" /> - <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> - <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> - <param name="own_file" value="bowtie2-ref.fasta" /> - <param name="sam_options_selector" value="yes" /> - <param name="reorder" value="true" /> + <conditional name="library"> + <param name="type" value="paired_collection"/> + <conditional name="paired_options"> + <param name="paired_options_selector" value="no"/> + </conditional> + <param name="unaligned_file" value="false"/> + <param name="input_1"> + <collection type="paired"> + <element name="forward" value="bowtie2-fq1.fa" ftype="fasta" /> + <element name="reverse" value="bowtie2-fq2.fa" ftype="fasta" /> + </collection> + </param> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="simple"/> + </conditional> + <conditional name="reference_genome"> + <param name="source" value="history" /> + <param name="own_file" value="bowtie2-ref.fasta" /> + </conditional> + <conditional name="sam_options"> + <param name="sam_options_selector" value="yes" /> + <param name="reorder" value="true" /> + </conditional> <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" lines_diff="4"> <metadata name="sort_order" value="unsorted"/> </output> </test> + <!-- test on fasta paired-end datasets with sam as output --> <test expect_num_outputs="1"> - <!-- test on fasta paired-end datasets with sam as output --> - <param name="type" value="paired"/> - <param name="paired_options_selector" value="no"/> - <param name="unaligned_file" value="false"/> - <param name="analysis_type_selector" value="simple"/> - <param name="source" value="history" /> - <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/> - <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/> - <param name="own_file" value="bowtie2-ref.fasta" /> - <param name="sam_options_selector" value="yes" /> - <param name="sam_options|sam_opt" value="true" /> + <conditional name="library"> + <param name="type" value="paired_collection"/> + <conditional name="paired_options"> + <param name="paired_options_selector" value="no"/> + </conditional> + <param name="unaligned_file" value="false"/> + <param name="input_1"> + <collection type="paired"> + <element name="forward" value="bowtie2-fq1.fa" ftype="fasta" /> + <element name="reverse" value="bowtie2-fq2.fa" ftype="fasta" /> + </collection> + </param> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="simple"/> + </conditional> + <conditional name="reference_genome"> + <param name="source" value="history" /> + <param name="own_file" value="bowtie2-ref.fasta" /> + </conditional> + <conditional name="sam_options"> + <param name="sam_options_selector" value="yes" /> + <param name="sam_opt" value="true" /> + </conditional> <output name="output" ftype="sam"> <metadata name="sort_order" value="unsorted"/> <assert_contents>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie2_indices.loc Wed Sep 24 13:37:14 2025 +0000 @@ -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 ${__HERE__}/bowtie2-ref \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Sep 24 13:37:14 2025 +0000 @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the Bowtie2 mapper format --> + <table name="bowtie2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/bowtie2_indices.loc" /> + </table> +</tables>