Mercurial > repos > erasmus-medical-center > dr_disco
changeset 1:9495360713d4 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b
| author | erasmus-medical-center |
|---|---|
| date | Thu, 16 Mar 2017 04:24:23 -0400 |
| parents | fca9c1ace23c |
| children | 173ca9768e22 |
| files | dr-disco_bam-extract.xml dr-disco_bam_extract.xml dr-disco_detect.xml dr-disco_fix.xml dr-disco_intronic.xml macros.xml test-data/detect.bam test-data/detect.txt test-data/fix_test-01.bam test-data/fix_test-01.fixed.bam |
| diffstat | 10 files changed, 122 insertions(+), 108 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dr-disco_bam-extract.xml Thu Mar 16 04:24:23 2017 -0400 @@ -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 detect_errors="exit_code"><![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 ${input_alignment.name}" /> + </outputs> + + <tests> + <test> + <param name="input_alignment" value="bam_extract.bam" /> + <param name="region1" value="chr21:39737183-40035618" /> + <param name="region2" value="chr21:42834478-42882085" /> + + <output name="output" file="bam_extract.bam" /> + </test> + <test> + <param name="input_alignment" value="bam_extract.bam" /> + <param name="region1" value="chr22:39737183-40035618" /> + <param name="region2" value="chr11:42834478-42882085" /> + + <output name="output" file="bam_extract.empty.bam" /> + </test> + </tests> + + <help> +Extract reads from two chromosomal positions (and also takes mates with the same name) + +Regions are in the format: + chr1:123-546 + </help> + + <expand macro="citations"/> +</tool>
--- a/dr-disco_bam_extract.xml Wed Jan 25 08:06:06 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,51 +0,0 @@ -<tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@-g0"> - <description>Extracts reads from two targeted regions</description> - <macros> - <import>macros.xml</import> - </macros> - - <expand macro="requirements" /> - <expand macro="version_command"/> - - <command><![CDATA[ - dr-disco bam-extract - '$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 ${input_alignment.name}" /> - </outputs> - - <tests> - <test> - <param name="input_alignment" value="bam_extract.bam" /> - <param name="region1" value="chr21:39737183-40035618" /> - <param name="region2" value="chr21:42834478-42882085" /> - - <output name="output" file="bam_extract.bam" /> - </test> - <test> - <param name="input_alignment" value="bam_extract.bam" /> - <param name="region1" value="chr22:39737183-40035618" /> - <param name="region2" value="chr11:42834478-42882085" /> - - <output name="output" file="bam_extract.empty.bam" /> - </test> - </tests> - - <help> -Extract reads from two chromosomal positions (and also takes mates with the same name) - -Regions are in the format: - chr1:123-546 - </help> - - <expand macro="citations"/> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dr-disco_detect.xml Thu Mar 16 04:24:23 2017 -0400 @@ -0,0 +1,41 @@ +<tool id="dr_disco_intronic" name="Dr. Disco (intronic)" version="@TOOL_VERSION@-g0"> + <description>Detects break-points in RNA-seq</description> + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="version_command"/> + + <command detect_errors="exit_code"><![CDATA[ + dr-disco + detect + --min-e-score '${min_e_score}' + '${table_fusion_events}' + '${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" argument="--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="table_fusion_events" format="tabular" label="${tool.name} on ${$star_discordant_alignment_fixed.name}" /> + </outputs> + + <tests> + <test> + <param name="star_discordant_alignment_fixed" value="detect.bam" /> + <param name="min_e_score" value="8" /> + + <output name="table_fusion_events" file="detect.txt" /> + </test> + </tests> + + <help><![CDATA[ + detects + ]]></help> + + <expand macro="citations"/> +</tool> \ No newline at end of file
--- a/dr-disco_fix.xml Wed Jan 25 08:06:06 2017 -0500 +++ b/dr-disco_fix.xml Thu Mar 16 04:24:23 2017 -0400 @@ -1,26 +1,36 @@ <tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@-g0"> - <description>Fixes and annotates chimeric alignments</description> + <description>Fixes chimeric alignments from STAR</description> <macros> <import>macros.xml</import> </macros> - + <expand macro="requirements" /> <expand macro="version_command" /> - - <command><![CDATA[ - dr-disco fix '${output}' '${star_discordant_alignment}' + + <command detect_errors="exit_code"><![CDATA[ + dr-disco fix '${alignment_fixed}' '${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 ${star_discordant_alignment}" /> + <data name="alignment_fixed" format="bam" label="${tool.name} on ${star_discordant_alignment}" /> </outputs> + <tests> + <test> + <param name="star_discordant_alignment" value="fix_test-01.bam"/> + + <output name="alignment_fixed" file="fix_test-01.fixed.bam" /> + </test> </tests> - <help> - </help> - + <help><![CDATA[ + +**What it does** + +Dr. Disco fix prepares chimeric alignment files produced by STAR for analysis with Dr. Disco (extract) and for visualization in genome browsers. + + ]]></help> <expand macro="citations"/> </tool> \ No newline at end of file
--- a/dr-disco_intronic.xml Wed Jan 25 08:06:06 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -<tool id="dr_disco_intronic" name="Dr. Disco (intronic)" version="@TOOL_VERSION@-g0"> - <description>Detects break-points in RNA-seq</description> - <macros> - <import>macros.xml</import> - </macros> - - <expand macro="requirements"/> - <expand macro="version_command"/> - - <command><![CDATA[ - ## old thing that evolved as such - depending on what the future will bring leave it out or include it... - touch empty.txt && - - dr-disco - intronic - -m '${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
--- a/macros.xml Wed Jan 25 08:06:06 2017 -0500 +++ b/macros.xml Thu Mar 16 04:24:23 2017 -0400 @@ -1,12 +1,12 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.2.0">dr-disco</requirement> + <requirement type="package" version="0.3.4">dr-disco</requirement> <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">0.2.0</token> + <token name="@TOOL_VERSION@">0.3.4</token> <xml name="version_command"> <version_command>dr-disco --version | head -n 1</version_command> @@ -15,13 +15,13 @@ <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> + <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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/detect.txt Thu Mar 16 04:24:23 2017 -0400 @@ -0,0 +1,2 @@ +chr-A pos-A direction-A chr-B pos-B direction-B filter-status intronic/exonic score soft+hardclips n-split-reads n-discordant-reads n-edges n-nodes-A n-nodes-B n-splice-junc-A n-splice-junc-B entropy-bp-edge entropy-all-edges data-structure +chr21 39877811 - chr21 42873374 + n_discordant_reads=0<1,n_support=3<8 intronic 9 6 3 0 1 1 1 0 0 1.0 1.0 chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(spanning_paired_1_t:3,spanning_paired_2_t:3)