Mercurial > repos > nilesh > rseqc
diff RPKM_count.xml @ 32:580ee0c4bc4e
Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
| author | lparsons |
|---|---|
| date | Mon, 07 Oct 2013 15:01:13 -0400 |
| parents | cc5eaa9376d8 |
| children |
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--- a/RPKM_count.xml Wed Oct 02 02:20:04 2013 -0400 +++ b/RPKM_count.xml Mon Oct 07 15:01:13 2013 -0400 @@ -1,75 +1,75 @@ -<tool id="RPKM_count" name="RPKM Count" version="1.1"> - <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description> - <requirements> - <requirement type="package" version="1.7.1">numpy</requirement> - <requirement type="package" version="2.3.7">rseqc</requirement> - </requirements> +<tool id="rseqc_RPKM_count" name="RPKM Count" version="1.1"> + <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description> + <requirements> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="2.3.7">rseqc</requirement> + </requirements> <command> ln -s "${input}" "local_input.bam" && ln -s "${input.metadata.bam_index}" "local_input.bam.bai" && RPKM_count.py -i "local_input.bam" -o output -r $refgene - #if str($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 $skiphits - -u - #end if - - #if $onlyexonic - -e - #end if + #if str($strand_type.strand_specific) == "pair" + -d + #if str($strand_type.pair_type) == "sd" + '1++,1--,2+-,2-+' + #else + '1+-,1-+,2++,2--' + #end if + #end if - </command> - <inputs> - <param name="input" type="data" format="bam" label="input bam/sam file" /> - <param name="refgene" type="data" format="bed" label="Reference gene model" /> - <conditional name="strand_type"> - <param name="strand_specific" type="select" label="Strand-specific?" value="None"> - <option value="none">None</option> - <option value="pair">Pair-End RNA-seq</option> - <option value="single">Single-End RNA-seq</option> - </param> - <when value="pair"> - <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" value="sd"> - <option value="sd"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option> - <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option> - </param> - </when> - <when value="single"> - <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" value="s"> - <option value="s">positive --> positive; negative --> negative</option> - <option value="d">positive --> negative; negative --> positive</option> - </param> - </when> - <when value="none"></when> - </conditional> - <param name="skiphits" type="boolean" value="false" label="Skip Multiple Hit Reads" /> - <param name="onlyexonic" type="boolean" value="false" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" /> - </inputs> - <outputs> - <data format="xls" name="outputxls" from_work_dir="output_read_count.xls"/> - </outputs> + #if str($strand_type.strand_specific) == "single" + -d + #if str($strand_type.single_type) == "s" + '++,--' + #else + '+-,-+' + #end if + #end if + + #if $skiphits + -u + #end if + + #if $onlyexonic + -e + #end if + + </command> <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> + <inputs> + <param name="input" type="data" format="bam" label="input bam/sam file" /> + <param name="refgene" type="data" format="bed" label="Reference gene model" /> + <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> + <param name="skiphits" type="boolean" value="false" label="Skip Multiple Hit Reads" /> + <param name="onlyexonic" type="boolean" value="false" label="Only use exonic (UTR exons and CDS exons) reads, otherwise use all reads" /> + </inputs> + <outputs> + <data format="xls" name="outputxls" from_work_dir="output_read_count.xls"/> + </outputs> + <help> RPKM_count.py +++++++++++++ @@ -83,22 +83,22 @@ ++++++++++++++ Input BAM/SAM file - Alignment file in BAM/SAM format. + Alignment file in BAM/SAM format. Reference gene model - Gene model in BED format. + Gene model in BED format. Strand sequencing type (default=none) - See Infer Experiment tool if uncertain. + See Infer Experiment tool if uncertain. Options ++++++++++++++ Skip Multiple Hit Reads - Use Multiple hit reads or use only uniquely mapped reads. + Use Multiple hit reads or use only uniquely mapped reads. Only use exonic reads - Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads. + Renders program only used exonic (UTR exons and CDS exons) reads, otherwise use all reads. Sample Output ++++++++++++++ @@ -113,7 +113,7 @@ chr1 29313959 29314417 NM_001166007_exon_2 0 '+' 1699 4 74.158 0.175 chr1 29319841 29320054 NM_001166007_exon_3 0 '+' 528 1 49.554 0.094 ===== ======== ======== ===================== ===== =========== ============= ============= ======== ========= - + ----- About RSeQC @@ -128,5 +128,5 @@ .. _RSeQC: http://rseqc.sourceforge.net/ - </help> + </help> </tool>