| Previous changeset 6:6202ec8aab61 (2015-07-21) Next changeset 8:758594ed0364 (2016-05-09) |
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Commit message:
planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d |
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modified:
tophat2_wrapper.xml |
| b |
| diff -r 6202ec8aab61 -r 4eb3c3beb9c7 tophat2_wrapper.xml --- a/tophat2_wrapper.xml Tue Jul 21 16:02:24 2015 -0400 +++ b/tophat2_wrapper.xml Fri Oct 09 15:48:52 2015 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="tophat2" name="Tophat" version="0.9">\n+<tool id="tophat2" name="TopHat" version="0.9">\n <!-- Wrapper compatible with Tophat version 2.0.0+ -->\n <description>Gapped-read mapper for RNA-seq data</description>\n <version_command>tophat2 --version</version_command>\n@@ -25,7 +25,7 @@\n ##\n \n tophat2\n- \n+\n ## Change this to accommodate the number of threads you have available.\n --num-threads \\${GALAXY_SLOTS:-4}\n \n@@ -35,7 +35,7 @@\n #if str($params.bowtie_n) == "Yes":\n --bowtie-n\n #end if\n- \n+\n --read-edit-dist $params.read_edit_dist\n --read-realign-edit-dist $params.read_realign_edit_dist\n -a $params.anchor_length\n@@ -48,7 +48,7 @@\n --segment-mismatches $params.seg_mismatches\n --segment-length $params.seg_length\n --library-type $params.library_type\n- \n+\n ## Indel search.\n #if $params.indel_search.allow_indel_search == "Yes":\n ## --allow-indels\n@@ -78,11 +78,11 @@\n #else:\n --no-coverage-search\n #end if\n- \n+\n #if str($params.microexon_search) == "Yes":\n --microexon-search\n #end if\n- \n+\n #if $params.fusion_search.do_search == "Yes":\n --fusion-search\n --fusion-anchor-length $params.fusion_search.anchor_len\n@@ -92,13 +92,13 @@\n --fusion-multipairs $params.fusion_search.multipairs\n --fusion-ignore-chromosomes "$params.fusion_search.ignore_chromosomes"\n #end if\n- \n+\n #if $params.bowtie2_settings.b2_settings == "Yes":\n #if $params.bowtie2_settings.preset.b2_preset == "Yes":\n --b2-$params.bowtie2_settings.preset.b2_preset_select\n- #end if \n+ #end if\n #end if\n- \n+\n #end if\n \n ## Read group information.\n@@ -113,7 +113,7 @@\n #if $singlePaired.sPaired != "single"\n -r $singlePaired.mate_inner_distance\n --mate-std-dev=$singlePaired.mate_std_dev\n- \n+\n #if str($singlePaired.report_discordant_pairs) == "No":\n --no-discordant\n #end if\n@@ -127,7 +127,7 @@\n ${index_path} "$singlePaired.input1"\n #end if\n </command>\n- \n+\n <inputs>\n <conditional name="singlePaired">\n <param name="sPaired" type="select" label="Is this single-end or paired-end data?">\n@@ -203,13 +203,13 @@\n </when>\n <when value="No" />\n </conditional>\n- \n+\n <!-- Microexon search params -->\n <param name="microexon_search" type="select" label="Use Microexon Search" help="--microexon-search; With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.">\n <option value="No">No</option>\n <option value="Yes">Yes</option>\n </param>\n- \n+\n <!-- Fusion mapping. -->\n <conditional name="fusion_search">\n <param name="do_search" type="select" label="Do Fusion Search" help="Reads can be aligned to potential fusion transcripts if the --fusion-search option is specified. The fusion alignments are reported in SAM format using custom fields XF and XP (see the output format) and some additional information about fusions will be reported (see fusions.out). Once mapping is done, you can run tophat-fusion-post to filter out fusion transcripts (see the TopHat-Fusion website for more details).">\n@@ -226,7 +226,7 @@\n <param name="ignore_chromosomes" type="text" value=\'\' label="--fusion-ignore-chromosomes; Ignore some chromosomes such as chrM whe'..b'n.\n - accepted_hits -- A list of read alignments in BAM_ format.\n@@ -568,27 +567,27 @@\n \n -------\n \n-**Tophat settings**\n+**TopHat settings**\n \n-All of the options have a default value. You can change any of them. Some of the options in Tophat have been implemented here.\n+All of the options have a default value. You can change any of them. Some of the options in TopHat have been implemented here.\n \n ------\n \n-**Tophat parameter list**\n+**TopHat parameter list**\n \n-This is a list of implemented Tophat options::\n+This is a list of implemented TopHat options::\n \n- -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments \n- selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter \n+ -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments\n+ selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter\n is required for paired end runs.\n --mate-std-dev INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.\n- -a/--min-anchor-length INT The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced \n- alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one \n+ -a/--min-anchor-length INT The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced\n+ alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one\n read with this many bases on each side. This must be at least 3 and the default is 8.\n -m/--splice-mismatches INT The maximum number of mismatches that may appear in the "anchor" region of a spliced alignment. The default is 0.\n -i/--min-intron-length INT The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart. The default is 70.\n -I/--max-intron-length INT The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read. The default is 500000.\n- -g/--max-multihits INT Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many \n+ -g/--max-multihits INT Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many\n alignments. The default is 40.\n -G/--GTF [GTF 2.2 file] Supply TopHat with a list of gene model annotations. TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping.\n -j/--raw-juncs [juncs file] Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-], left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive.\n' |