Mercurial > repos > erasmus-medical-center > dr_disco
changeset 0:fca9c1ace23c draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a
| author | erasmus-medical-center |
|---|---|
| date | Wed, 25 Jan 2017 08:06:06 -0500 |
| parents | |
| children | 9495360713d4 |
| files | dr-disco_bam_extract.xml dr-disco_fix.xml dr-disco_intronic.xml macros.xml test-data/bam_extract.bam test-data/bam_extract.empty.bam |
| diffstat | 6 files changed, 144 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dr-disco_bam_extract.xml Wed Jan 25 08:06:06 2017 -0500 @@ -0,0 +1,51 @@ +<tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@-g0"> + <description>Extracts reads from two targeted regions</description> + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements" /> + <expand macro="version_command"/> + + <command><![CDATA[ + dr-disco bam-extract + '$region1' + '$region2' + '$output' + '$input_alignment' + ]]></command> + <inputs> + <param name="input_alignment" type="data" format="bam" label="Discordant alignment file of STAR)" /> + <param name="region1" type="text" value="chr21:39737183-40035618" label="Genomic region 1" /> + <param name="region2" type="text" value="chr21:42834478-42882085" label="Genomic region 2" /> + </inputs> + <outputs> + <data name="output" format="bam" label="${tool.name} on ${input_alignment.name}" /> + </outputs> + + <tests> + <test> + <param name="input_alignment" value="bam_extract.bam" /> + <param name="region1" value="chr21:39737183-40035618" /> + <param name="region2" value="chr21:42834478-42882085" /> + + <output name="output" file="bam_extract.bam" /> + </test> + <test> + <param name="input_alignment" value="bam_extract.bam" /> + <param name="region1" value="chr22:39737183-40035618" /> + <param name="region2" value="chr11:42834478-42882085" /> + + <output name="output" file="bam_extract.empty.bam" /> + </test> + </tests> + + <help> +Extract reads from two chromosomal positions (and also takes mates with the same name) + +Regions are in the format: + chr1:123-546 + </help> + + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dr-disco_fix.xml Wed Jan 25 08:06:06 2017 -0500 @@ -0,0 +1,26 @@ +<tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@-g0"> + <description>Fixes and annotates chimeric alignments</description> + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements" /> + <expand macro="version_command" /> + + <command><![CDATA[ + dr-disco fix '${output}' '${star_discordant_alignment}' + ]]></command> + <inputs> + <param name="star_discordant_alignment" type="data" format="bam" label="Discordant alignment file of STAR" /> + </inputs> + <outputs> + <data name="output" format="bam" label="${tool.name} on ${star_discordant_alignment}" /> + </outputs> + <tests> + </tests> + + <help> + </help> + + <expand macro="citations"/> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dr-disco_intronic.xml Wed Jan 25 08:06:06 2017 -0500 @@ -0,0 +1,39 @@ +<tool id="dr_disco_intronic" name="Dr. Disco (intronic)" version="@TOOL_VERSION@-g0"> + <description>Detects break-points in RNA-seq</description> + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="version_command"/> + + <command><![CDATA[ + ## old thing that evolved as such - depending on what the future will bring leave it out or include it... + touch empty.txt && + + dr-disco + intronic + -m '${min_e_score}' + '${output}' + empty.txt + '${star_discordant_alignment_fixed}' + ]]></command> + <inputs> + <param name="star_discordant_alignment_fixed" type="data" format="bam" label="Discordant alignment file of STAR (processed with dr-disco fix)" /> + <param name="min_e_score" type="integer" value="8" min="0" + label="Minimal score to initiate pulling sub-graphs" + help="Larger numbers boost performance but result in suboptimal results. Values of 8 and below are considered to be very safe (this corresponds to initiate merging already from clusters that consist of 2 or 3 reads)." /> + </inputs> + + <outputs> + <data name="output" format="tabular" label="${tool.name} on ${$star_discordant_alignment_fixed.name}" /> + </outputs> + + <tests> + </tests> + + <help> + </help> + + <expand macro="citations"/> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jan 25 08:06:06 2017 -0500 @@ -0,0 +1,28 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.2.0">dr-disco</requirement> + <yield/> + </requirements> + </xml> + + <token name="@TOOL_VERSION@">0.2.0</token> + + <xml name="version_command"> + <version_command>dr-disco --version | head -n 1</version_command> + </xml> + + <xml name="citations"> + <citations> + <!--<citation type="doi"></citation>--> + <citation type="bibtex"> + @unpublished{dr_disco, + author = {Youri Hoogstrate}, + title = {Dr. Disco: detecting genomic breakpoints of TMPRSS2-ERG in prostate cancer using RNA-Seq data only}, + url = {https://github.com/yhoogstrate/dr-disco} + } + </citation> + <yield /> + </citations> + </xml> +</macros> \ No newline at end of file