| Previous changeset 2:c1ec08cb34f9 (2014-12-12) Next changeset 4:1fc845afa3ac (2015-07-21) |
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Commit message:
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modified:
bowtie2_wrapper.xml tool_dependencies.xml |
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| diff -r c1ec08cb34f9 -r ceb6467e276c bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Fri Dec 12 11:12:27 2014 -0500 +++ b/bowtie2_wrapper.xml Mon Mar 09 11:58:43 2015 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="bowtie2" name="Bowtie2" version="0.3">\n+<tool id="bowtie2" name="Bowtie2" version="0.4">\n <!-- Wrapper compatible with Bowtie version 2.2.4 -->\n <description>- map reads against reference genome</description>\n <version_command>bowtie2 --version</version_command>\n@@ -31,13 +31,13 @@\n \n ## Fastq inputs\n #if str( $library.type ) == "single":\n- -U "${input_1}"\n+ -U "${library.input_1}"\n #if str( $library.unaligned_file ) == "true":\n --un $output_unaligned_reads_l\n #end if\n #elif str( $library.type ) == "paired":\n- -1 "${input_1}"\n- -2 "${input_2}"\n+ -1 "${library.input_1}"\n+ -2 "${library.input_2}"\n #if str( $library.paired_options.paired_options_selector ) == "yes":\n -I "${library.paired_options.I}"\n -X "${library.paired_options.X}"\n@@ -88,32 +88,34 @@\n --trim5 "${analysis_type.input_options.trim5}"\n --trim3 "${analysis_type.input_options.trim3}"\n ${analysis_type.input_options.qv_encoding}\n- ${analysis_type.input_options.solexa-quals}\n- ${analysis_type.input_options.int-quals}\n+ ${analysis_type.input_options.solexa_quals}\n+ ${analysis_type.input_options.int_quals}\n #end if\n \n #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":\n- -N "${$analysis_type.alignment_options.N}"\n- -L "${$analysis_type.alignment_options.L}"\n- -i "${$analysis_type.alignment_options.i}"\n- --n_ceil "${$analysis_type.alignment_options.n_ceil}"\n- --dpad "${$analysis_type.alignment_options.dpad}"\n- --gbar "${$analysis_type.alignment_options.gbar}"\n- ${analysis_type.alignment_options.ignore-quals}\n+ -N "${analysis_type.alignment_options.N}"\n+ -L "${analysis_type.alignment_options.L}"\n+ -i "${analysis_type.alignment_options.i}"\n+ --n-ceil "${analysis_type.alignment_options.n_ceil}"\n+ --dpad "${analysis_type.alignment_options.dpad}"\n+ --gbar "${analysis_type.alignment_options.gbar}"\n+ ${analysis_type.alignment_options.ignore_quals}\n ${analysis_type.alignment_options.nofw}\n ${analysis_type.alignment_options.norc}\n ${analysis_type.alignment_options.no_1mm_upfront}\n #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":\n --end-to-end\n- --score-min "${$analysis_type.alignment_options.align_mode.core-min}"\n+ --score-min "${analysis_type.alignment_options.align_mode.score_min_ete}"\n #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":\n --local\n- --score-min "${$analysis_type.alignment_options.align_mode.core-min}"\n+ --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}"\n #end if\n #end if\n \n #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":\n- --ma "${analysis_type.scoring_options.ma}"\n+ #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):\n+ --ma "${analysis_type.scoring_options.ma}"\n+ #end if\n --mp "${analysis_type.scoring_options.mp}"\n --np "${analysis_type.scoring_options.np}"\n --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}"\n@@ -132,13'..b'attempt to find either an exact or a 1-mismatch\n- end-to-end alignment for the read *before* trying the [multiseed heuristic]. Such\n+ end-to-end alignment for the read *before* trying the multiseed heuristic. Such\n alignments can be found very quickly, and many short read alignments have exact or\n near-exact end-to-end alignments. However, this can lead to unexpected\n- alignments when the user also sets options governing the [multiseed heuristic],\n+ alignments when the user also sets options governing the multiseed heuristic,\n like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal\n to the length of the read, the user will be surprised to find 1-mismatch alignments\n reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end\n- alignments before using the [multiseed heuristic], which leads to the expected\n+ alignments before using the multiseed heuristic, which leads to the expected\n behavior when combined with options such as `-L` and `-N`. This comes at the\n expense of speed.\n \n@@ -721,8 +722,7 @@\n Sets a function governing the minimum alignment score needed for an alignment to\n be considered "valid" (i.e. good enough to report). This is a function of read\n length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`\n- to `f(x) = 0 + -0.6 * x`, where `x` is the read length. See also: [setting\n- function options]. The default in `--end-to-end` mode is `L,-0.6,-0.6` and\n+ to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and\n the default in `--local` mode is `G,20,8`.\n \n ----- \n@@ -840,18 +840,15 @@\n --dovetail\n If the mates "dovetail", that is if one mate alignment extends past the\n beginning of the other such that the wrong mate begins upstream, consider that\n- to be concordant. See also: [Mates can overlap, contain or dovetail each\n- other]. Default: mates cannot dovetail in a concordant alignment.\n+ to be concordant. Default: mates cannot dovetail in a concordant alignment.\n \n --no-contain\n If one mate alignment contains the other, consider that to be non-concordant.\n- See also: [Mates can overlap, contain or dovetail each other]. Default: a mate\n- can contain the other in a concordant alignment.\n+ Default: a mate can contain the other in a concordant alignment.\n \n --no-overlap\n If one mate alignment overlaps the other at all, consider that to be\n- non-concordant. See also: [Mates can overlap, contain or dovetail each other]. \n- Default: mates can overlap in a concordant alignment.\n+ non-concordant. Default: mates can overlap in a concordant alignment.\n \n ------\n \n@@ -866,9 +863,9 @@\n --rg <text>\n Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the\n `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`\n- must also be specified. This is because the `ID` tag is required by the [SAM\n- Spec][SAM]. Specify `--rg` multiple times to set multiple fields. See the\n- [SAM Spec][SAM] for details about what fields are legal.\n+ must also be specified. This is because the `ID` tag is required by the SAM\n+ Specification. Specify `--rg` multiple times to set multiple fields. See the\n+ SAM Specification for details about what fields are legal.\n \n --omit-sec-seq\n When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`\n' |
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| diff -r c1ec08cb34f9 -r ceb6467e276c tool_dependencies.xml --- a/tool_dependencies.xml Fri Dec 12 11:12:27 2014 -0500 +++ b/tool_dependencies.xml Mon Mar 09 11:58:43 2015 -0400 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="bowtie2" version="2.2.4"> - <repository changeset_revision="2b25b6e8d108" name="package_bowtie_2_2_4" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="172979b6bf77" name="package_bowtie_2_2_4" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.18"> <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> |