Mercurial > repos > nilesh > rseqc
diff bam2wig.xml @ 32:580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
| author | lparsons |
|---|---|
| date | Mon, 07 Oct 2013 15:01:13 -0400 |
| parents | cc5eaa9376d8 |
| children | 8fbd165f8835 |
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--- a/bam2wig.xml Wed Oct 02 02:20:04 2013 -0400 +++ b/bam2wig.xml Mon Oct 07 15:01:13 2013 -0400 @@ -1,92 +1,101 @@ -<tool id="bam2wig" name="BAM to Wiggle" version="1.1"> - <description> - converts all types of RNA-seq data from .bam to .wig - </description> - <requirements> - <requirement type="package" version="2.11.0">R</requirement> - <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="2.3.7">rseqc</requirement> - </requirements> - <command> - ln -s "${input}" "local_input.bam" && - ln -s "${input.metadata.bam_index}" "local_input.bam.bai" && - bam2wig.py -i "local_input.bam" -s $chromsize -o outfile +<tool id="rseqc_bam2wig" name="BAM to Wiggle" version="1.1"> + <description> + converts all types of RNA-seq data from .bam to .wig + </description> + <requirements> + <requirement type="package" version="3.0.1">R</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="2.3.7">rseqc</requirement> + </requirements> + <command> + + #import tempfile, os + #set $tmp_input = tempfile.NamedTemporaryFile() + #set $tmp_input_name = $input_singles_tmp_handle.name + #silent $tmp_input.close() + + ln -s "${input}" $tmp_input_name && + ln -s "${input.metadata.bam_index}" $tmp_input_name + ".bai" && + bam2wig.py -i "local_input.bam" -s $chromsize -o outfile - #if str($strand_type.strand_specific) == "pair" - -d - #if str($strand_type.pair_type) == "sd" - '1++,1--,2+-,2-+' - #else - '1+-,1-+,2++,2--' - #end if - #end if + #if str($strand_type.strand_specific) == "pair" + -d + #if str($strand_type.pair_type) == "sd" + '1++,1--,2+-,2-+' + #else + '1+-,1-+,2++,2--' + #end if + #end if - #if str($strand_type.strand_specific) == "single" - -d - #if str($strand_type.single_type) == "s" - '++,--' - #else - '+-,-+' - #end if - #end if + #if str($strand_type.strand_specific) == "single" + -d + #if str($strand_type.single_type) == "s" + '++,--' + #else + '+-,-+' + #end if + #end if - #if $wigsum.wigsum_type - -t $wigsum.totalwig - #end if + #if $wigsum.wigsum_type + -t $wigsum.totalwig + #end if - #if $skipmultihits - -u - #end if - </command> - <inputs> - <param name="input" type="data" label="Input .bam File" format="bam" /> - <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" /> - <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" /> - <conditional name="wigsum"> - <param name="wigsum_type" type="boolean" label="Specify wigsum?" value="false"> - </param> - <when value="true"> - <param name="totalwig" value="0" type="integer" label="specified wigsum" /> - </when> - <when value="false"></when> - </conditional> - <conditional name="strand_type"> - <param name="strand_specific" type="select" label="Strand-specific?" value="none"> - <option value="none">none</option> - <option value="pair">Pair-End RNA-seq</option> - <option value="single">Single-End RNA-seq</option> - </param> - <when value="pair"> - <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd"> - <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option> - <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option> - </param> - </when> - <when value="single"> - <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s"> - <option value="s">positive --> positive; negative --> negative</option> - <option value="d">positive --> negative; negative --> positive</option> - </param> - </when> - <when value="none"></when> - </conditional> - </inputs> - <outputs> - <data format="wig" name="output" from_work_dir="outfile.wig"> - <filter>strand_type['strand_specific'] == 'none'</filter> - </data> - <data format="wig" name="outputfwd" from_work_dir="outfile_Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)"> - <filter>strand_type['strand_specific'] != 'none'</filter> - </data> - <data format="wig" name="outputrv" from_work_dir="outfile_Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)"> - <filter>strand_type['strand_specific'] != 'none'</filter> - </data> - </outputs> + #if $skipmultihits + -u + #end if + ; + rm $tmp_input_name + ".bai" ; + rm $tmp_input_name + </command> + <inputs> + <param name="input" type="data" label="Input .bam File" format="bam" /> + <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" /> + <param name="skipmultihits" type="boolean" label="Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads" value="false" /> + <conditional name="wigsum"> + <param name="wigsum_type" type="boolean" label="Specify wigsum?" value="false"> + </param> + <when value="true"> + <param name="totalwig" value="0" type="integer" label="specified wigsum" /> + </when> + <when value="false"/> + </conditional> + <conditional name="strand_type"> + <param name="strand_specific" type="select" label="Strand-specific?" value="none"> + <option value="none">none</option> + <option value="pair">Pair-End RNA-seq</option> + <option value="single">Single-End RNA-seq</option> + </param> + <when value="pair"> + <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd"> + <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option> + <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option> + </param> + </when> + <when value="single"> + <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s"> + <option value="s">positive --> positive; negative --> negative</option> + <option value="d">positive --> negative; negative --> positive</option> + </param> + </when> + <when value="none"></when> + </conditional> + </inputs> + <outputs> + <data format="wig" name="output" from_work_dir="outfile.wig"> + <filter>strand_type['strand_specific'] == 'none'</filter> + </data> + <data format="wig" name="outputfwd" from_work_dir="outfile_Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)"> + <filter>strand_type['strand_specific'] != 'none'</filter> + </data> + <data format="wig" name="outputrv" from_work_dir="outfile_Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)"> + <filter>strand_type['strand_specific'] != 'none'</filter> + </data> + </outputs> <stdio> <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> </stdio> - <help> + <help> bam2wig.py ++++++++++ @@ -103,19 +112,19 @@ ++++++++++++++ Input BAM file - Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools. + Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools. Chromosome size file - Tab or space separated text file with 2 columns: first column is chromosome name, second column is size of the chromosome. Chromosome names (such as "chr1") should be consistent between this file and BAM file. + Tab or space separated text file with 2 columns: first column is chromosome name, second column is size of the chromosome. Chromosome names (such as "chr1") should be consistent between this file and BAM file. Specified wigsum (default=none) - Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization. + Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization. Skip multiple Hit reads - skips multiple hit reads or only use uniquely mapped reads + skips multiple hit reads or only use uniquely mapped reads Strand-specific (default=none) - How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py + How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py Outputs ++++++++++++++ @@ -143,5 +152,5 @@ .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1 - </help> + </help> </tool>