| Previous changeset 6:09a7281d24c5 (2015-07-21) Next changeset 8:ca29c55c78e7 (2015-11-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd |
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modified:
bwa-mem.xml bwa.xml bwa_macros.xml read_group_macros.xml tool_dependencies.xml |
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| diff -r 09a7281d24c5 -r d8c9597bfb09 bwa-mem.xml --- a/bwa-mem.xml Tue Jul 21 14:12:49 2015 -0400 +++ b/bwa-mem.xml Tue Nov 03 09:36:45 2015 -0500 |
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| @@ -1,14 +1,11 @@ <?xml version="1.0"?> -<tool id="bwa_mem" name="Map with BWA-MEM" version="0.3.1"> +<tool id="bwa_mem" name="Map with BWA-MEM" version="0.4.1"> <description>- map medium and long reads (> 100 bp) against reference genome</description> <macros> <import>read_group_macros.xml</import> <import>bwa_macros.xml</import> </macros> - <requirements> - <requirement type="package" version="0.7.10.039ea20639">bwa</requirement> - <requirement type="package" version="1.1">samtools</requirement> - </requirements> + <expand macro="requirements" /> <expand macro="stdio" /> <command> #set $reference_fasta_filename = "localref.fa" @@ -170,7 +167,7 @@ <when value="paired"> <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/> <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/> - <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both "250" and "250,25" will work while "250,,10" will not. See below for details."> + <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both "250" and "250,25" will work while "250,,10" will not. See below for details."> <sanitizer invalid_char=""> <valid initial="string.digits"><add value=","/> </valid> </sanitizer> @@ -181,7 +178,7 @@ </when> <when value="paired_collection"> <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> - <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both "250" and "250,25" will work while "250,,10" will not. See below for details."> + <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both "250" and "250,25" will work while "250,,10" will not. See below for details."> <sanitizer invalid_char=""> <valid initial="string.digits"><add value=","/> </valid> </sanitizer> @@ -189,7 +186,7 @@ </when> <when value="paired_iv"> <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> - <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both "250" and "250,25" will work while "250,,10" will not. See below for details."> + <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both "250" and "250,25" will work while "250,,10" will not. See below for details."> <sanitizer invalid_char=""> <valid initial="string.digits"><add value=","/> </valid> </sanitizer> |
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| diff -r 09a7281d24c5 -r d8c9597bfb09 bwa.xml --- a/bwa.xml Tue Jul 21 14:12:49 2015 -0400 +++ b/bwa.xml Tue Nov 03 09:36:45 2015 -0500 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="bwa" name="Map with BWA" version="0.3.1"> +<tool id="bwa" name="Map with BWA" version="0.4.1"> <description>- map short reads (< 100 bp) against reference genome</description> <macros> <import>read_group_macros.xml</import> @@ -65,11 +65,7 @@ </when> </xml> </macros> - - <requirements> - <requirement type="package" version="0.7.10.039ea20639">bwa</requirement> - <requirement type="package" version="1.1">samtools</requirement> - </requirements> + <expand macro="requirements" /> <expand macro="stdio" /> <command> #set $reference_fasta_filename = "localref.fa" |
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| diff -r 09a7281d24c5 -r d8c9597bfb09 bwa_macros.xml --- a/bwa_macros.xml Tue Jul 21 14:12:49 2015 -0400 +++ b/bwa_macros.xml Tue Nov 03 09:36:45 2015 -0500 |
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| @@ -1,20 +1,27 @@ <macros> <import>read_group_macros.xml</import> <token name="@set_rg_string@"> - #set $rg_string = "@RG\tID:" + str($rg_id) - #set $rg_string += $format_read_group("\tSM:", $rg_sm) - #set $rg_string += $format_read_group("\tPL:", $rg_pl) - #set $rg_string += $format_read_group("\tLB:", $rg_lb) - #set $rg_string += $format_read_group("\tCN:", $rg_cn) - #set $rg_string += $format_read_group("\tDS:", $rg_ds) - #set $rg_string += $format_read_group("\tDT:", $rg_dt) - #set $rg_string += $format_read_group("\tFO:", $rg_fo) - #set $rg_string += $format_read_group("\tKS:", $rg_ks) - #set $rg_string += $format_read_group("\tPG:", $rg_pg) - #set $rg_string += $format_read_group("\tPI:", $rg_pi) - #set $rg_string += $format_read_group("\tPU:", $rg_pu) + #set $rg_string = "@RG\\tID:" + str($rg_id) + #set $rg_string += $format_read_group("\\tSM:", $rg_sm) + #set $rg_string += $format_read_group("\\tPL:", $rg_pl) + #set $rg_string += $format_read_group("\\tLB:", $rg_lb) + #set $rg_string += $format_read_group("\\tCN:", $rg_cn) + #set $rg_string += $format_read_group("\\tDS:", $rg_ds) + #set $rg_string += $format_read_group("\\tDT:", $rg_dt) + #set $rg_string += $format_read_group("\\tFO:", $rg_fo) + #set $rg_string += $format_read_group("\\tKS:", $rg_ks) + #set $rg_string += $format_read_group("\\tPG:", $rg_pg) + #set $rg_string += $format_read_group("\\tPI:", $rg_pi) + #set $rg_string += $format_read_group("\\tPU:", $rg_pu) </token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.7.10.039ea20639">bwa</requirement> + <requirement type="package" version="1.2">samtools</requirement> + </requirements> + </xml> + <xml name="stdio"> <stdio> <exit_code range="1:" /> |
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| diff -r 09a7281d24c5 -r d8c9597bfb09 read_group_macros.xml --- a/read_group_macros.xml Tue Jul 21 14:12:49 2015 -0400 +++ b/read_group_macros.xml Tue Nov 03 09:36:45 2015 -0500 |
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| @@ -146,7 +146,7 @@ </when> </xml> <xml name="read_group_id_param"> - <param name="ID" type="text" value="" size="20" 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" optional="false"> <validator type="empty_field" /> </param> </xml> @@ -158,7 +158,7 @@ </conditional> </xml> <xml name="read_group_sm_param"> - <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" 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" /> </xml> <xml name="read_group_sm_conditional"> <conditional name="read_group_sm_conditional"> @@ -171,7 +171,7 @@ as per Picard. --> <xml name="read_group_sm_param_required"> - <param name="SM" type="text" value="" size="20" 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)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced"> <validator type="empty_field" /> </param> </xml> @@ -194,7 +194,7 @@ </param> </xml> <xml name="read_group_lb_param"> - <param name="LB" type="text" size="25" label="Library name (LB)" optional="true" /> + <param name="LB" type="text" label="Library name (LB)" optional="true" /> </xml> <xml name="read_group_lb_conditional"> <conditional name="read_group_lb_conditional"> @@ -204,7 +204,7 @@ </conditional> </xml> <xml name="read_group_lb_required_param"> - <param name="LB" type="text" size="25" label="Library name (LB)" optional="false"> + <param name="LB" type="text" label="Library name (LB)" optional="false"> <validator type="empty_field" /> </param> </xml> @@ -216,33 +216,33 @@ </conditional> </xml> <xml name="read_group_cn_param"> - <param name="CN" type="text" size="25" label="Sequencing center that produced the read (CN)" /> + <param name="CN" type="text" label="Sequencing center that produced the read (CN)" /> </xml> <xml name="read_group_ds_param"> - <param name="DS" type="text" size="25" label="Description (DS)" /> + <param name="DS" type="text" label="Description (DS)" /> </xml> <xml name="read_group_dt_param"> - <param name="DT" type="text" size="25" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" /> + <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" size="25" 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]+/"> + <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> </xml> <xml name="read_group_ks_param"> - <param name="KS" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" /> + <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" /> </xml> <xml name="read_group_pg_param"> - <param name="PG" type="text" size="25" label="Programs used for processing the read group (PG)" /> + <param name="PG" type="text" label="Programs used for processing the read group (PG)" /> </xml> <xml name="read_group_pi_param"> <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" size="25" 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)" optional="True" /> </xml> <xml name="read_group_pu_required_param"> - <param name="PU" type="text" size="25" 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)" optional="False" /> </xml> <!-- Only ID is required - all groups available --> <xml name="read_group_inputs_spec"> |
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| diff -r 09a7281d24c5 -r d8c9597bfb09 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jul 21 14:12:49 2015 -0400 +++ b/tool_dependencies.xml Tue Nov 03 09:36:45 2015 -0500 |
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| @@ -3,7 +3,7 @@ <package name="bwa" version="0.7.10.039ea20639"> <repository changeset_revision="5b9aca1e1c07" name="package_bwa_0_7_10_039ea20639" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="samtools" version="1.1"> - <repository changeset_revision="f0c7bc0159e9" name="package_samtools_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |