1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5215215c3659/ changeset: r5128:5215215c3659 user: kanwei date: 2011-02-25 19:35:27 summary: Typos affected #: 4 files (21 bytes) --- a/tools/filters/fileGrep.xml Thu Feb 24 19:07:41 2011 -0500 +++ b/tools/filters/fileGrep.xml Fri Feb 25 13:35:27 2011 -0500 @@ -1,19 +1,19 @@ -<tool id="fileGrep1" name="Match"> - <description>a column from one Query against another Query</description> - <command>cut -f $col $input1 | grep -f - $match $input2 > $out_file1</command> - <inputs> - <param name="col" size="2" type="text" value="1" label="Match content of column"/> - <param format="tabular" name="input1" type="data" label="From Query1"/> +<tool id="fileGrep1" name="Match"> + <description>a column from one Query against another Query</description> + <command>cut -f $col $input1 | grep -f - $match $input2 > $out_file1</command> + <inputs> + <param name="col" size="2" type="text" value="1" label="Match content of column"/> + <param format="tabular" name="input1" type="data" label="From Query1"/><param format="tabular" name="input2" type="data" label="Against Query2"/> - <param name="match" type="select" label="and return rows that"> - <option value="">Match</option> - <option value="-v">Do not match</option> - </param> - </inputs> - <outputs> + <param name="match" type="select" label="and return rows that"> + <option value="">Match</option> + <option value="-v">Do not match</option> + </param> + </inputs> + <outputs><data format="input" name="out_file1" metadata_source="input2" /> - </outputs> - <help> + </outputs> + <help> This tool is based on UNIX command grep with option -f. It matches content of one query against another. For example, assume you have two queries - one that contains EST accession numbers and some other information:: AA001229 12 12 @@ -32,11 +32,11 @@ chr7 115443243 115443347 DB331869_exon_0_0_chr7_115443244_f 0 + chr7 115443347 115443373 DB331869_exon_1_0_chr7_115443348_f 0 + -Using this tool you will bne able to tell how many ESTs in Query1 are also preset in Query2 and will output this:: +Using this tool you will be able to tell how many ESTs in Query1 are also preset in Query2 and will output this:: chr7 115443239 115443802 AA001842_exon_0_0_chr7_115443240_f 0 if **Match** option is chosen. -</help> +</help></tool> \ No newline at end of file --- a/tools/ngs_rna/cuffdiff_wrapper.xml Thu Feb 24 19:07:41 2011 -0500 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Fri Feb 25 13:35:27 2011 -0500 @@ -209,7 +209,7 @@ 1. Transcript FPKM expression tracking. 2. Gene FPKM expression tracking; tracks the summed FPKM of transcripts sharing each gene_id 3. Primary transcript FPKM tracking; tracks the summed FPKM of transcripts sharing each tss_id -4. Coding sequence FPKM tracking; tracks the summed FPKM of transcripts sharing each p_id, indepedent of tss_id +4. Coding sequence FPKM tracking; tracks the summed FPKM of transcripts sharing each p_id, independent of tss_id 5. Transcript differential FPKM. 6. Gene differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each gene_id 7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id @@ -233,7 +233,7 @@ -m INT This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 45bp. -s INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. -Q Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0. - -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads). + -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads). --FDR FLOAT The allowed false discovery rate. The default is 0.05. --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000 --max-mle-iterations INT Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000 --- a/tools/ngs_rna/tophat_wrapper.xml Thu Feb 24 19:07:41 2011 -0500 +++ b/tools/ngs_rna/tophat_wrapper.xml Fri Feb 25 13:35:27 2011 -0500 @@ -25,7 +25,7 @@ ## First input file always required. --input1=$singlePaired.input1 - ## Set parms based on whether reads are single-end or paired. + ## Set params based on whether reads are single-end or paired. #if $singlePaired.sPaired == "single": --settings=$singlePaired.sParams.sSettingsType #if $singlePaired.sParams.sSettingsType == "full": @@ -171,7 +171,7 @@ <option value="full">Full parameter list</option></param><when value="preSet" /> - <!-- Full/advanced parms. --> + <!-- Full/advanced params. --><when value="full"><param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol."><option value="fr-unstranded">FR Unstranded</option> @@ -277,7 +277,7 @@ <option value="full">Full parameter list</option></param><when value="preSet" /> - <!-- Full/advanced parms. --> + <!-- Full/advanced params. --><when value="full"><param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol."><option value="fr-unstranded">FR Unstranded</option> @@ -435,7 +435,7 @@ <test><!-- Tophat commands: bowtie-build -f test-data/tophat_in1.fasta tophat_in1 - tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 ++allow-indels +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger + tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +allow-indels +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger Replace the + with double-dash --><param name="genomeSource" value="history"/> --- a/tools/sr_mapping/lastz_wrapper.xml Thu Feb 24 19:07:41 2011 -0500 +++ b/tools/sr_mapping/lastz_wrapper.xml Fri Feb 25 13:35:27 2011 -0500 @@ -504,7 +504,7 @@ up 65 thousand --census32[=<output_file>] count and report how many times each target bas aligns, up to 4 billion - --writecapsule=<capsule_file> just write out a targegt capsule file and quit; don't + --writecapsule=<capsule_file> just write out a target capsule file and quit; don't search for seeds or perform subsequent stages --verbosity=<level> set info level (0 is minimum, 10 is everything) (default is 0) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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