| Previous changeset 2:8afd8a379d5f (2015-07-21) |
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Commit message:
planemo upload commit 4ec9eb1570ea116d83f5464a786af6e14fb5b57d |
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modified:
tophat_wrapper.xml |
| b |
| diff -r 8afd8a379d5f -r 2ad64c5bb5f4 tophat_wrapper.xml --- a/tophat_wrapper.xml Tue Jul 21 16:01:00 2015 -0400 +++ b/tophat_wrapper.xml Fri Oct 09 15:48:13 2015 -0400 |
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| b'@@ -1,5 +1,5 @@\n-<tool id="tophat" name="Tophat for Illumina" version="1.5.0">\n- <!-- Wrapper compatible with Tophat versions 1.3.0 to 1.4.1 -->\n+<tool id="tophat" name="TopHat for Illumina" version="1.5.0">\n+ <!-- Wrapper compatible with TopHat versions 1.3.0 to 1.4.1 -->\n <description>Find splice junctions using RNA-seq data</description>\n <version_command>tophat --version</version_command>\n <requirements>\n@@ -43,7 +43,7 @@\n --seg-mismatches=$singlePaired.sParams.seg_mismatches\n --seg-length=$singlePaired.sParams.seg_length\n --library-type=$singlePaired.sParams.library_type\n- \n+\n ## Indel search.\n #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes":\n ## --allow-indels\n@@ -104,7 +104,7 @@\n --seg-mismatches=$singlePaired.pParams.seg_mismatches\n --seg-length=$singlePaired.pParams.seg_length\n --library-type=$singlePaired.pParams.library_type\n- \n+\n ## Indel search.\n #if $singlePaired.pParams.indel_search.allow_indel_search == "Yes":\n ## --allow-indels\n@@ -181,25 +181,14 @@\n <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />\n <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />\n <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="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." />\n- <conditional name="indel_search">\n- <param name="allow_indel_search" type="select" label="Allow indel search">\n- <option value="Yes">Yes</option>\n- <option value="No">No</option>\n- </param>\n- <when value="No"/>\n- <when value="Yes">\n- <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />\n- <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />\n- </when>\n- </conditional>\n-alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />\n+ <expand macro="indel_searchConditional" />\n <param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />\n <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />\n <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />\n <param name="initial_read_mismatches" type="integer" min="0" value="2" label="Number of mismatches allowed in the initial read mapping" />\n <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />\n <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />\n- \n+\n <!-- Options for supplying own junctions. -->\n <conditional name="own_junctions">\n '..b'n.\n - accepted_hits -- A list of read alignments in BAM_ format.\n@@ -519,27 +508,27 @@\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' |