Mercurial > repos > iuc > bedtools
changeset 10:c78cf6fe3018 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
| author | iuc |
|---|---|
| date | Mon, 03 Oct 2016 07:36:08 -0400 |
| parents | 2ab422b551df |
| children | 7308cc546a36 |
| files | all_fasta.loc.sample bamToFastq.xml getfastaBed.xml maskFastaBed.xml multiCov.xml shuffleBed.xml tool_data_table_conf.xml.sample unionBedGraphs.xml |
| diffstat | 8 files changed, 57 insertions(+), 16 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Mon Oct 03 07:36:08 2016 -0400 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- a/bamToFastq.xml Wed Sep 14 17:30:10 2016 -0400 +++ b/bamToFastq.xml Mon Oct 03 07:36:08 2016 -0400 @@ -16,8 +16,8 @@ </command> <inputs> <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/> - <param name="tags" type="boolean" truevalue="-tags" falsevalue="" selected="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/> - <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" selected="False" label="FASTQ for second end. + <param name="tags" type="boolean" truevalue="-tags" falsevalue="" checked="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/> + <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="False" label="FASTQ for second end. Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/> </inputs> <outputs>
--- a/getfastaBed.xml Wed Sep 14 17:30:10 2016 -0400 +++ b/getfastaBed.xml Mon Oct 03 07:36:08 2016 -0400 @@ -7,19 +7,38 @@ <expand macro="stdio" /> <command> <![CDATA[ + #if str( $fasta_source.fasta_source_selector ) == 'history': + #set $fasta_file = $fasta_source.fasta + #else + #set $fasta_file = $fasta_source.fasta_id.fields.path + #end if bedtools getfasta $name $tab $strand $split - -fi $fasta - -bed $input - -fo $output + -fi '$fasta_file' + -bed '$input' + -fo '$output' ]]> </command> <inputs> <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" /> - <param format="fasta" name="fasta" type="data" label="Fasta file" /> + + <conditional name="fasta_source"> + <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file"> + <option value="history" selected="True">History</option> + <option value="preloaded">Server indexed files</option> + </param> + <when value="history"> + <param name="fasta" format="fasta" type="data" label="Fasta file" /> + </when> + <when value="preloaded"> + <param name="fasta_id" type="select"> + <options from_data_table="all_fasta" /> + </param> + </when> + </conditional> <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue="" label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" help="(-name)" />
--- a/maskFastaBed.xml Wed Sep 14 17:30:10 2016 -0400 +++ b/maskFastaBed.xml Mon Oct 03 07:36:08 2016 -0400 @@ -21,7 +21,7 @@ <param name="soft" type="boolean" checked="false" truevalue="-soft" falsevalue="" label="Soft-mask (that is, convert to lower-case bases) the FASTA sequence" help="By default, hard-masking (that is, conversion to Ns) is performed. (-soft)" /> - <param name="mc" type="text" value="N" length="1" + <param name="mc" type="text" value="N" label="Replace masking character" help="That is, instead of masking with Ns, use another character. (-mc)" /> </inputs>
--- a/multiCov.xml Wed Sep 14 17:30:10 2016 -0400 +++ b/multiCov.xml Mon Oct 03 07:36:08 2016 -0400 @@ -55,7 +55,7 @@ <tests> <test> <param name="input" value="multiCov1.bed" ftype="bed" /> - <param name="bams" value="srma_in3.bam,srma_in3.bam" ftpye="bam"/> + <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/> <param name="q" value="1"/> <param name="split" value="False"/> <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
--- a/shuffleBed.xml Wed Sep 14 17:30:10 2016 -0400 +++ b/shuffleBed.xml Mon Oct 03 07:36:08 2016 -0400 @@ -30,9 +30,9 @@ </command> <inputs> <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> - <param name="bedpe" type="boolean" label="The file is in BEDPE format" selected="False" truevalue="-bedpe" falsevalue="" /> + <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" /> <expand macro="genome" /> - <param name="chrom" type="boolean" selected="False" truevalue="-chrom" falsevalue="" + <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue="" label="Keep features in the input file on the same chromosome" help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" /> <expand macro="seed" /> @@ -51,14 +51,14 @@ <param name="incl" type="data" format="bed" label="Choose File" /> </when> </conditional> - <param name="chromfirst" type="boolean" selected="False" truevalue="-chromFirst" falsevalue="" + <param name="chromfirst" type="boolean" checked="False" truevalue="-chromFirst" falsevalue="" label="Choose chromosome first" help="Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size. (-chromFirst)" /> <param name="maxtries" type="integer" value="1000" label="Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl" help="(-maxTries)" /> - <param name="no_overlap" type="boolean" selected="False" truevalue="-noOverlapping" falsevalue="" + <param name="no_overlap" type="boolean" checked="False" truevalue="-noOverlapping" falsevalue="" label="Don’t allow shuffled intervals to overlap" help="(-noOverlapping)" /> - <param name="allow_beyond" type="boolean" selected="False" truevalue="-allowBeyondChromEnd" falsevalue="" + <param name="allow_beyond" type="boolean" checked="False" truevalue="-allowBeyondChromEnd" falsevalue="" label="Allow the original the length of the original records to extebd beyond the length of the chromosome" help="(-allowBeyondChromEnd)" /> </inputs> <outputs>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Oct 03 07:36:08 2016 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables>
--- a/unionBedGraphs.xml Wed Sep 14 17:30:10 2016 -0400 +++ b/unionBedGraphs.xml Mon Oct 03 07:36:08 2016 -0400 @@ -105,9 +105,6 @@ This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files. -.. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/ubg.png - - .. class:: warningmark This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file).