| Previous changeset 11:546ada4a9f43 (2016-01-19) Next changeset 13:53646aaaafef (2017-01-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a |
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modified:
bwa-mem.xml bwa.xml bwa_macros.xml |
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removed:
tool_dependencies.xml |
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| diff -r 546ada4a9f43 -r bd3a1e0de84c bwa-mem.xml --- a/bwa-mem.xml Tue Jan 19 11:20:59 2016 -0500 +++ b/bwa-mem.xml Fri Dec 30 08:11:12 2016 -0500 |
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| @@ -26,6 +26,10 @@ #if str( $analysis_type.analysis_type_selector ) == "pacbio": -x pacbio + #elif str( $analysis_type.analysis_type_selector ) == "ont2d": + -x ont2d + #elif str( $analysis_type.analysis_type_selector ) == "intractg": + -x intractg #elif str( $analysis_type.analysis_type_selector ) == "full": #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set": ## Algorithmic options -k "${analysis_type.algorithmic_options.k}" @@ -96,9 +100,7 @@ "${fastq_input.fastq_input1}" #end if - | samtools view -Sb - > temporary_bam_file.bam && - - samtools sort -f temporary_bam_file.bam ${bam_output} + | samtools sort -O bam -o '$bam_output' ]]> </command> @@ -147,7 +149,9 @@ <param name="analysis_type_selector" type="select" label="Select analysis mode"> <option value="illumina">1.Simple Illumina mode</option> <option value="pacbio">2.PacBio mode (-x pacbio)</option> - <option value="full">3.Full list of options</option> + <option value="ont2d">3.Nanopore 2D-reads mode (-x ont2d)</option> + <option value="intractg">4.Intra-species contigs mode (-x intractg)</option> + <option value="full">5.Full list of options</option> </param> <when value="illumina"> <!-- do nothing --> @@ -155,6 +159,12 @@ <when value="pacbio"> <!-- do nothing. all magic happens within <command> tag --> </when> + <when value="ont2d"> + <!-- do nothing. all magic happens within <command> tag --> + </when> + <when value="intractg"> + <!-- do nothing. all magic happens within <command> tag --> + </when> <when value="full"> <conditional name="algorithmic_options"> <param name="algorithmic_options_selector" type="select" label="Set algorithmic options?" help="Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e options."> |
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| diff -r 546ada4a9f43 -r bd3a1e0de84c bwa.xml --- a/bwa.xml Tue Jan 19 11:20:59 2016 -0500 +++ b/bwa.xml Fri Dec 30 08:11:12 2016 -0500 |
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| @@ -218,9 +218,7 @@ "${reference_fasta_filename}" first.sai "${input_type.bam_input}" #end if - | samtools view -Sb - > temporary_bam_file.bam && - - samtools sort -f temporary_bam_file.bam ${bam_output} + | samtools sort -O bam -o '$bam_output' ]]> </command> |
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| diff -r 546ada4a9f43 -r bd3a1e0de84c bwa_macros.xml --- a/bwa_macros.xml Tue Jan 19 11:20:59 2016 -0500 +++ b/bwa_macros.xml Fri Dec 30 08:11:12 2016 -0500 |
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| @@ -1,7 +1,7 @@ <macros> <import>read_group_macros.xml</import> - <token name="@VERSION@">0.7.12</token> + <token name="@VERSION@">0.7.15</token> <token name="@set_rg_string@"> #set $rg_string = "@RG\\tID:" + str($rg_id) @@ -35,7 +35,7 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">bwa</requirement> - <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="1.3.1">samtools</requirement> </requirements> </xml> @@ -174,9 +174,9 @@ 2. https://www.biostars.org/ 3. https://github.com/lh3/bwa 4. http://bio-bwa.sourceforge.net/ - + </token> - + <token name="@dataset_collections@"> ------ |
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| diff -r 546ada4a9f43 -r bd3a1e0de84c tool_dependencies.xml --- a/tool_dependencies.xml Tue Jan 19 11:20:59 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bwa" version="0.7.12"> - <repository changeset_revision="6af9b24ddeee" name="package_bwa_0_7_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <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> |