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Changeset 9:b21145d59d9c (2017-01-23)

Previous changeset 8:8366a8c82a7a (2016-02-08)

Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/fuma commit 7bf6f3629e96bcaaed8770badd11366889efa99c

modified:
fuma.xml
test-data/edgren_test_01_specifc_matching_output.txt
test-data/edgren_test_02_unspecifc_matching_output.txt

added:
test-data/edgren_test_03_specific_matching_output.txt
test-data/edgren_test_04_unspecific_matching_output.txt

removed:
tool_dependencies.xml

diff -r 8366a8c82a7a -r b21145d59d9c fuma.xml
--- a/fuma.xml Mon Feb 08 04:56:40 2016 -0500
+++ b/fuma.xml Mon Jan 23 09:41:08 2017 -0500

[

b'@@ -1,14 +1,13 @@\n <?xml version="1.0" encoding="UTF-8"?>\n-<tool id="fuma" name="FuMa" version="2.11.3-g0">\n+<tool id="fuma" name="FuMa" version="3.0.5-g0">\n <description>match detected fusion genes based on gene names (in particular for RNA-Seq)</description>\n- \n+\n <requirements>\n- <requirement type="package" version="2.7">python</requirement>\n- <requirement type="package" version="2.11.3">fuma</requirement>\n+ <requirement type="package" version="3.0.5">fuma</requirement>\n </requirements>\n- \n+\n <version_command>fuma --version 2>&1 | head -n 1</version_command>\n- \n+\n <command><![CDATA[\n #import pipes\n \n@@ -25,9 +24,9 @@\n #set $links = $links + [ $sample_name + ":" + str("ga_") + str($i) ]\n #end for\n \n- #set $gene_annotations_str = " ".join(gene_annotations)\n- #set $samples_str = " ".join(samples)\n- #set $links_str = " ".join(links)\n+ #set $gene_annotations_str = "\'"+"\' \'".join(gene_annotations)+"\'"\n+ #set $samples_str = "\'"+"\' \'".join(samples)+"\'"\n+ #set $links_str = "\'"+"\' \'".join(links)+"\'"\n \n fuma \n -m\n@@ -49,12 +48,12 @@\n #else\n -f $params.output_format.value\n #end if\n- -o $fuma_overview ; \n+ -o \'${fuma_overview}\'\n \n \n #if $params.output_format.value == "list_boolean"\n- fuma-list-to-boolean-list -o tmp.txt $fuma_overview ;\n- mv tmp.txt $fuma_overview\n+ && fuma-list-to-boolean-list -o tmp.txt \'${fuma_overview}\'\n+ && mv tmp.txt \'${fuma_overview}\'\n #end if\n ]]></command>\n \n@@ -94,7 +93,9 @@\n <param name="long_gene_size" type="hidden" value="200000" />\n </when>\n <when value="full">\n- <param name="matching_method" type="select" label="Matching method: technique used to match fusion genes based on annotated gene sets" help="Overlap is the most sensitive but also more sensitive for long gene artefacts; subset is the recommended technique and EGM is conservative">\n+ <param name="matching_method" type="select" label="Matching method: technique used to match fusion genes based on annotated gene sets"\n+ help="Overlap is the most sensitive but also more sensitive for long gene artefacts; subset is the recommended technique and EGM is conservative"\n+ argument="-m">\n <option value="overlap">Overlap</option>\n <option value="subset" selected="True">Subset</option>\n <option value="egm">Exact Geneset Matching (EGM)</option>\n@@ -111,7 +112,9 @@\n label="Consider fusion genes distinct when the donor and acceptor sites are swapped (A,B) != (B,A)"\n help="This settings is not recommended when fusion genes detected in DNA-Seq are used" />\n \n- <param name="long_gene_size" type="integer" min="0" value="200000" label="Long gene size" help="Gene-name based matching is more sensitive to long genes. This is the gene size used to mark fusion genes spanning a \'long gene\' as reported the output. Use 0 to disable this feature (--long-gene-size)" />\n+ <param name="long_gene_size" type="integer" min="0" value="200000" label="Long gene size"\n+ help="Gene-name based matching is more sensitive to long genes. This is the gene size used to mark fusion genes spanning a \'long gene\' as reported the output. Use 0 to disable this feature"\n+ argument="--long-gene-size" />\n \n <param name="output_format" type="select" label="Output format">\n <option value="list_boolean" selected="true">List (Boolean)</option>\n@@ -127,27 +130,70 @@\n </outputs>\n \n <tests>\n+ \n+ <test>\n+ <param name="datasets_0|sample" value="edgren_fusion-map.txt" ftype="tabular" />\n+ <param name="datasets_0|format" value="fusionmap" />\n+ <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n+\n+ <param name="datasets_1|sample" value="edgren_true_positives.txt" ftype="tabular" />\n+ <param name="datasets_1|format" value="fusionmap" />\n+ <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n \n <param name="settingsType" value="full" />\n \n@@ -157,29 +203,16 @@\n <param name="long_gene_size" value="200000" />\n <param name="output_format" value="list_boolean" />\n \n- <output name="fuma_overview" file="edgren_test_01_specifc_matching_output.txt" />\n+ <output name="fuma_overview" file="edgren_test_03_specific_matching_output.txt" />\n </test>\n <test>\n- \n- <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" />\n- <param name="datasets_0|format" value="chimerascan" />\n- <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n- \n- \n- <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" />\n- <param name="datasets_1|format" value="defuse" />\n- <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n- \n- \n- <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" />\n- <param name="datasets_2|format" value="fusionmap" />\n- <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n- \n- \n- <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" />\n- <param name="datasets_3|format" value="fusionmap" />\n- <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n- \n+ <param name="datasets_0|sample" value="edgren_fusion-map.txt" ftype="tabular" />\n+ <param name="datasets_0|format" value="fusionmap" />\n+ <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n+\n+ <param name="datasets_1|sample" value="edgren_true_positives.txt" ftype="tabular" />\n+ <param name="datasets_1|format" value="fusionmap" />\n+ <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n \n <param name="settingsType" value="full" />\n \n@@ -189,7 +222,7 @@\n <param name="long_gene_size" value="200000" />\n <param name="output_format" value="list_boolean" />\n \n- <output name="fuma_overview" file="edgren_test_02_unspecifc_matching_output.txt" />\n+ <output name="fuma_overview" file="edgren_test_04_unspecific_matching_output.txt" />\n </test>\n </tests>\n \n'

diff -r 8366a8c82a7a -r b21145d59d9c test-data/edgren_test_01_specifc_matching_output.txt
--- a/test-data/edgren_test_01_specifc_matching_output.txt Mon Feb 08 04:56:40 2016 -0500
+++ b/test-data/edgren_test_01_specifc_matching_output.txt Mon Jan 23 09:41:08 2017 -0500

b'@@ -1,651 +1,314 @@\n Left-genes\tRight-genes\tSpans large gene (>200000bp)\tedgren_chimerascan.txt\tedgren_defuse.txt\tedgren_fusion-map.txt\tedgren_true_positives.txt\n-NR_037945:STX16\tRAE1\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-TPD52L2\tDNAJC5\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-C20orf112\tC20orf112\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-PREX1\tCPNE1:NM_001198863:NR_037188\tTRUE\tTRUE\tFALSE\tFALSE\tFALSE\n-AP5S1\tMAVS:NR_037921\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-BCAS4\tNM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-NR_036633:VAPB\tAPCDD1L-AS1\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_037945:STX16\tRAE1\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+C20orf112\tC20orf112\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+BCAS4\tNM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n CSNK2A1\tFAM110A:NM_001289145:NM_001289146:NM_001289147\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n NR_109859\tAP5S1\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n FKBP1A:NR_037661:SDCBP2-AS1\tLOC284801\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-ADNP:NM_001282531\tRSPO4\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-LAMA5\tLOC284801\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-OSER1-AS1\tOSER1-AS1\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n+ADNP:NM_001282531\tRSPO4\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n ZFP64\tNM_001281507:PHACTR3\tTRUE\tTRUE\tFALSE\tFALSE\tFALSE\n-ARFGAP1:NM_001281482:NM_001281483:NM_001281484:NR_104022:NR_104023\tIFT52:NM_001303458:NM_001303459\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-RAD21L1\tHMGN1\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n+ARFGAP1:NM_001281482:NM_001281483:NM_001281484:NR_104022:NR_104023\tIFT52:NM_001303458:NM_001303459\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n VPS16\tPCP4\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-ATP5O\tKIF16B\tTRUE\tTRUE\tFALSE\tFALSE\tFALSE\n-PCNT\tADNP:NM_001282531:NM_001282532\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-SLC2A4RG\tBRWD1\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-LOC400927:NM_001289912\tNR_110051:ZNF217\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-LOC284801\tTUBGCP6\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n+ATP5O\tKIF16B\tTRUE\tTRUE\tFALSE\tFALSE\tTRUE\n+LOC400927:NM_001289912\tNR_110051:ZNF217\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n ELMO2\tJOSD1\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-RTCB\tSTMN3\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-HIRA\tNM_001282933:NM_001282935:NR_104259:NR_110623:ZNF341\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-DENND6B\tMTRNR2L3:RAE1\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-EWSR1\tNM_001278649:OSBPL2\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-CTSZ\tEP300\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n+RTCB\tSTMN3\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n DYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tLARGE\tTRUE\tTRUE\tFALSE\tFALSE\tFALSE\n ENTPD6\tNM_001287387:SLC25A1\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-SHANK3\tLAMA5\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-ATRN\tNM_001284277:NM_001284278:PITPNB\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n+SHANK3\tLAMA5\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n SULF2\tPRICKLE2:PRICKLE2-AS1\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-VPRBP\tNSFL1C\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-MFN1\tMAPRE1\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-PCMTD2\tPAK2\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-CEP63\tDNMT3B\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-RRP9\tCSE1L\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-CP:NR_046371\tCHD6\tTRUE\tTRUE\tFALSE\tFALSE\tFALSE\n-TMEM189:TMEM189-UBE2V1\tGLT8D1:GNL3:NM_001278280:NM_001278281\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-ST6GAL1\tNM_001278649:OSBPL2\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-OXSM\tMAP1LC3A\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-PHF20\tCDC25A\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-GOLIM4:NM_001308155\tGNAS:NM_001309840:NM_001309861\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-SLC25A38\tNM_001301188:NM_001301190:NM_001301193:NM_001301196:NM_001301201:TRIB3\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-ZNFX1\tIQCG\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-SNRK\tLAMA5\tFALSE\tTRUE\tFALSE\tFALSE\tFALSE\n-EYA2\tNR_103507:SLC6A6\tTRUE\tTRUE\tFALSE\tFALSE\tFALSE\n+VPRBP\tNSFL1C\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+CEP63\tDNMT3B\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+ST6GAL1\tNM_001278649:OSBPL2\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+GOLIM4:NM_001308155\tGNAS:NM_001309840:NM_001309861\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+SNRK\tLAMA5\tFALSE\tTR'..b'ARD14\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n-PDCD2\tRPL26\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n-EIF2A\tMYH11:NDE1\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n-GATAD2A\tGATAD2A:NM_001300946\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n+PDCD2\tRPL26\tFALSE\tFALSE\tFALSE\tTRUE\tTRUE\n PLD3\tNM_001291311:PLD3\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n-ARFIP1:NM_001287431:NM_001287432:NM_001287433\tDPY19L3\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n-EEF1A1\tZNF317\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n-NR_031672:SPTAN1\tBCL2L13:NR_073068:NR_073069\tTRUE\tFALSE\tFALSE\tTRUE\tFALSE\n-HMGN2\tESYT1\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n+ARFIP1:NM_001287431:NM_001287432:NM_001287433\tDPY19L3\tFALSE\tFALSE\tFALSE\tTRUE\tTRUE\n LOC644961:TMEM222\tACTG1:NR_037688\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n SARS\tME2\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n KISS1\tGOLT1A\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n@@ -11359,36 +5728,38 @@\n NM_001286052:NM_001286053:NM_001286054:NM_001289931:NR_110527:ZNF595:ZNF718\tPSPH\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n RALGPS1\tRALGPS1\tTRUE\tFALSE\tFALSE\tTRUE\tFALSE\n SULF2\tARFGEF2\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n-NDUFA1\tSYNJ2BP:SYNJ2BP-COX16\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n-NEDD8:NEDD8-MDP1\tNEDD8:NEDD8-MDP1\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n+NDUFA1\tSYNJ2BP:SYNJ2BP-COX16\tFALSE\tFALSE\tFALSE\tTRUE\tTRUE\n YLPM1\tITPK1\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\n LAMP1\tMCF2L2\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\n NFS1\tPREX1\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\n STARD3\tDOK5:NM_177959\tFALSE\tFALSE\tFALSE\tFALSE\tTRUE\n NM_001272060:RPS6KB1\tVMP1\tFALSE\tFALSE\tFALSE\tFALSE\tTRUE\n+GSDMB\tTATDN1\tFALSE\tTRUE\tFALSE\tTRUE\tFALSE\n+ACACA\tSTAC2\tTRUE\tTRUE\tFALSE\tTRUE\tFALSE\n+MED1\tACSF2:NM_001288968:NM_001288969:NM_001288970:NM_001288971:NM_001288972:NR_110232\tFALSE\tTRUE\tFALSE\tTRUE\tFALSE\n+VPS35\tPPP3R1\tFALSE\tTRUE\tFALSE\tTRUE\tFALSE\n NOS1AP\tC1orf226\tTRUE\tTRUE\tFALSE\tTRUE\tFALSE\n INIP\tC5\tFALSE\tTRUE\tFALSE\tTRUE\tFALSE\n-FAM208B\tFAM208B\tFALSE\tTRUE\tFALSE\tTRUE\tFALSE\n-MED1\tACSF2:NM_001288968:NM_001288969:NM_001288970:NM_001288971:NM_001288972:NR_110232\tFALSE\tTRUE\tFALSE\tTRUE\tFALSE\n-PPP3R1\tVPS35\tFALSE\tTRUE\tFALSE\tTRUE\tFALSE\n PPP1R12A\tSEPT10\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n-NM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tCEP250\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n-ARFGEF2\tSULF2\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n-DIDO1\tNM_001303457:TTI1\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n-DHX35\tITCH\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n CPNE1:NM_001198863:NR_037188\tPI3\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n-CCDC85C\tSETD3\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+ITCH\tDHX35\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+NM_001303457:TTI1\tDIDO1\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+CEP250\tNM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+SULF2\tARFGEF2\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+SETD3\tCCDC85C\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n CYTH1\tEIF3H\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n RARA\tPKIA\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n-BCAS4\tBCAS3\tTRUE\tTRUE\tFALSE\tFALSE\tTRUE\n-NR_036633:VAPB\tIKZF3:NM_001284514:NM_001284515\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n-NM_001272060:RPS6KB1\tSNF8\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n-SKA2\tMYO19\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+GSDMB\tTATDN1\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+GSDMB\tTATDN1\tFALSE\tFALSE\tFALSE\tTRUE\tTRUE\n+IKZF3:NM_001284514:NM_001284515\tNR_036633:VAPB\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+BCAS3\tBCAS4\tTRUE\tTRUE\tFALSE\tFALSE\tTRUE\n+ACACA\tSTAC2\tTRUE\tTRUE\tFALSE\tFALSE\tTRUE\n+ACACA\tSTAC2\tTRUE\tFALSE\tFALSE\tTRUE\tTRUE\n+SNF8\tNM_001272060:RPS6KB1\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+MYO19\tSKA2\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n BSG\tNFIX\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n-RAB22A\tMYO9B\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n-GLB1\tCMTM7\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n-NOTCH1\tNUP214\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n-WDR67\tZNF704\tTRUE\tTRUE\tFALSE\tFALSE\tTRUE\n+MYO9B\tRAB22A\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+CMTM7\tGLB1\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n ANKHD1:ANKHD1-EIF4EBP3\tPCDH1\tFALSE\tFALSE\tFALSE\tTRUE\tTRUE\n-TATDN1\tGSDMB\tFALSE\tTRUE\tFALSE\tTRUE\tTRUE\n-ACACA\tSTAC2\tTRUE\tTRUE\tFALSE\tTRUE\tTRUE\n+NUP214\tNOTCH1\tFALSE\tTRUE\tFALSE\tFALSE\tTRUE\n+ZNF704\tWDR67\tTRUE\tTRUE\tFALSE\tFALSE\tTRUE\n'

diff -r 8366a8c82a7a -r b21145d59d9c test-data/edgren_test_02_unspecifc_matching_output.txt
--- a/test-data/edgren_test_02_unspecifc_matching_output.txt Mon Feb 08 04:56:40 2016 -0500
+++ b/test-data/edgren_test_02_unspecifc_matching_output.txt Mon Jan 23 09:41:08 2017 -0500

@@ -11198,51 +11198,51 @@
LAMP1 MCF2L2 TRUE FALSE FALSE FALSE TRUE
NFS1 PREX1 TRUE FALSE FALSE FALSE TRUE
VMP1 NM_001272060:RPS6KB1 FALSE FALSE FALSE FALSE TRUE
+RAE1 NR_037945:STX16 FALSE TRUE TRUE FALSE FALSE
+CPNE1:NM_001198863:NR_037188 PREX1 TRUE TRUE TRUE FALSE FALSE
+TPD52L2 DNAJC5 FALSE TRUE TRUE FALSE FALSE
+SUMF1 LRRFIP2:NM_001282691 FALSE TRUE TRUE FALSE FALSE
+VAMP8 VAMP5 FALSE TRUE TRUE FALSE FALSE
+NM_001165931:RRM2 C2orf48 FALSE TRUE TRUE FALSE FALSE
+TMEM120A STYXL1 FALSE TRUE TRUE FALSE FALSE
+NCOA2 ZNF704 TRUE TRUE TRUE FALSE FALSE
FEN1 FADS2:NM_001281501:NM_001281502 FALSE TRUE TRUE FALSE FALSE
MCF2L LAMP1 FALSE TRUE TRUE FALSE FALSE
+TNFRSF1A SCNN1A FALSE TRUE TRUE FALSE FALSE
GCN1L1 MSI1 FALSE TRUE TRUE FALSE FALSE
-TNFRSF1A SCNN1A FALSE TRUE TRUE FALSE FALSE
-RAE1 NR_037945:STX16 FALSE TRUE TRUE FALSE FALSE
-TPD52L2 DNAJC5 FALSE TRUE TRUE FALSE FALSE
-CPNE1:NM_001198863:NR_037188 PREX1 TRUE TRUE TRUE FALSE FALSE
SYNRG TOB1 FALSE TRUE TRUE FALSE FALSE
MED1 STXBP4 FALSE TRUE TRUE FALSE FALSE
-SUMF1 LRRFIP2:NM_001282691 FALSE TRUE TRUE FALSE FALSE
-NM_001165931:RRM2 C2orf48 FALSE TRUE TRUE FALSE FALSE
-VAMP8 VAMP5 FALSE TRUE TRUE FALSE FALSE
-TMEM120A STYXL1 FALSE TRUE TRUE FALSE FALSE
-NCOA2 ZNF704 TRUE TRUE TRUE FALSE FALSE
FAM208B FAM208B FALSE TRUE FALSE TRUE FALSE
YAF2 RYBP FALSE TRUE FALSE TRUE FALSE
ARHGAP27:NM_001282290 ARHGAP27:NM_001282290 FALSE TRUE FALSE TRUE FALSE
VPS35 PPP3R1 FALSE TRUE FALSE TRUE FALSE
+HMGN2 ESYT1 FALSE TRUE FALSE TRUE FALSE
NOS1AP C1orf226 TRUE TRUE FALSE TRUE FALSE
KISS1 GOLT1A FALSE TRUE FALSE TRUE FALSE
CC2D1B DTYMK FALSE TRUE FALSE TRUE FALSE
-HMGN2 ESYT1 FALSE TRUE FALSE TRUE FALSE
INIP C5 FALSE TRUE FALSE TRUE FALSE
PPP1R12A SEPT10 FALSE TRUE FALSE FALSE TRUE
+CPNE1:NM_001198863:NR_037188 PI3 FALSE TRUE FALSE FALSE TRUE
ITCH DHX35 FALSE TRUE FALSE FALSE TRUE
-CPNE1:NM_001198863:NR_037188 PI3 FALSE TRUE FALSE FALSE TRUE
SETD3 CCDC85C FALSE TRUE FALSE FALSE TRUE
+STARD3 DOK5:NM_177959 FALSE FALSE TRUE FALSE TRUE
ZNF704 WDR67 TRUE TRUE FALSE FALSE TRUE
-STARD3 DOK5:NM_177959 FALSE FALSE TRUE FALSE TRUE
+NM_001303457:TTI1 DIDO1 FALSE TRUE TRUE FALSE TRUE
+CEP250 NM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8 FALSE TRUE TRUE FALSE TRUE
TEKT4P2 BRWD1 FALSE TRUE TRUE TRUE FALSE
+CMTM7 GLB1 FALSE TRUE TRUE FALSE TRUE
+NUP214 NOTCH1 FALSE TRUE TRUE FALSE TRUE
+IKZF3:NM_001284514:NM_001284515 NR_036633:VAPB FALSE TRUE TRUE FALSE TRUE
+BCAS3 BCAS4 TRUE TRUE TRUE FALSE TRUE
MED1 ACSF2:NM_001288968:NM_001288969:NM_001288970:NM_001288971:NM_001288972:NR_110232 FALSE TRUE TRUE TRUE FALSE
BCAS3 MED13 TRUE TRUE TRUE TRUE FALSE
-BSG NFIX FALSE TRUE TRUE FALSE TRUE
+SNF8 NM_001272060:RPS6KB1 FALSE TRUE TRUE FALSE TRUE
+CYTH1 EIF3H FALSE TRUE TRUE FALSE TRUE
MYO9B RAB22A FALSE TRUE TRUE FALSE TRUE
-NUP214 NOTCH1 FALSE TRUE TRUE FALSE TRUE
-CMTM7 GLB1 FALSE TRUE TRUE FALSE TRUE
-CEP250 NM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8 FALSE TRUE TRUE FALSE TRUE
-NM_001303457:TTI1 DIDO1 FALSE TRUE TRUE FALSE TRUE
-CYTH1 EIF3H FALSE TRUE TRUE FALSE TRUE
-BCAS3 BCAS4 TRUE TRUE TRUE FALSE TRUE
-IKZF3:NM_001284514:NM_001284515 NR_036633:VAPB FALSE TRUE TRUE FALSE TRUE
-SNF8 NM_001272060:RPS6KB1 FALSE TRUE TRUE FALSE TRUE
+BSG NFIX FALSE TRUE TRUE FALSE TRUE
ANKHD1:ANKHD1-EIF4EBP3 PCDH1 FALSE FALSE TRUE TRUE TRUE
SULF2 ARFGEF2 FALSE TRUE TRUE TRUE TRUE
+ACACA STAC2 TRUE TRUE TRUE TRUE TRUE
+MYO19 SKA2 FALSE TRUE TRUE TRUE TRUE
GSDMB TATDN1 FALSE TRUE TRUE TRUE TRUE
RARA PKIA FALSE TRUE TRUE TRUE TRUE
-ACACA STAC2 TRUE TRUE TRUE TRUE TRUE
-MYO19 SKA2 FALSE TRUE TRUE TRUE TRUE

diff -r 8366a8c82a7a -r b21145d59d9c test-data/edgren_test_03_specific_matching_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/edgren_test_03_specific_matching_output.txt Mon Jan 23 09:41:08 2017 -0500

@@ -0,0 +1,54 @@
+Left-genes Right-genes Spans large gene (>200000bp) edgren_fusion-map.txt edgren_true_positives.txt
+NR_120540 UBA2 FALSE TRUE FALSE
+NR_024091:ZFP91:ZFP91-CNTF LINC00261 FALSE TRUE FALSE
+FAT3 CASC5 TRUE TRUE FALSE
+FAM208B FAM208B FALSE TRUE FALSE
+FRMD4A FRMD4A TRUE TRUE FALSE
+NM_001291876:NM_001291877:TACC2 RPLP1 TRUE TRUE FALSE
+EEF1A1 GHITM FALSE TRUE TRUE
+RYBP YAF2 FALSE TRUE TRUE
+NM_001290002:NM_001290004:NR_120486:NR_120487:ZNF385A NR_120486:NR_120487:ZNF385A FALSE TRUE FALSE
+POR PUS1 FALSE TRUE TRUE
+NM_001293212:NM_001293213:NM_001293214:NM_001293215:NM_001293216:NR_120608:TUBB KRT80 FALSE TRUE TRUE
+HNRNPK AATF FALSE TRUE TRUE
+MYO19 SKA2 FALSE TRUE FALSE
+MED1 ACSF2:NM_001288968:NM_001288969:NM_001288970:NM_001288971:NM_001288972:NR_110232 FALSE TRUE FALSE
+ARHGAP27:NM_001282290 ARHGAP27:NM_001282290 FALSE TRUE FALSE
+BCAS3 MED13 TRUE TRUE FALSE
+BPTF AMZ2:NM_001289054:NM_001289056 FALSE TRUE FALSE
+CARD14 CARD14 FALSE TRUE FALSE
+PDCD2 RPL26 FALSE TRUE TRUE
+PLD3 NM_001291311:PLD3 FALSE TRUE FALSE
+ARFIP1:NM_001287431:NM_001287432:NM_001287433 DPY19L3 FALSE TRUE TRUE
+LOC644961:TMEM222 ACTG1:NR_037688 FALSE TRUE FALSE
+SARS ME2 FALSE TRUE FALSE
+NOS1AP C1orf226 TRUE TRUE FALSE
+KISS1 GOLT1A FALSE TRUE FALSE
+CC2D1B DTYMK FALSE TRUE FALSE
+SYTL1 HSP90AB1 FALSE TRUE FALSE
+PAK2 MAGEA10:MAGEA10-MAGEA5 FALSE TRUE FALSE
+TMCC1 TMCC1 TRUE TRUE FALSE
+HPS3:NM_001308258:NR_046371 CP:NR_046371 FALSE TRUE FALSE
+RSRC1 RSRC1 TRUE TRUE FALSE
+GREB1 GREB1 FALSE TRUE FALSE
+NR_130784 NR_037904:SCLY TRUE TRUE FALSE
+PNKD:TMBIM1 PNKD:TMBIM1 FALSE TRUE FALSE
+PTMA RGL2 FALSE TRUE FALSE
+SLC30A5 AZIN1:NM_001301668 FALSE TRUE FALSE
+NM_001286052:NM_001286053:NM_001286054:NM_001289931:NR_110527:ZNF595:ZNF718 PSPH FALSE TRUE FALSE
+INIP C5 FALSE TRUE FALSE
+RALGPS1 RALGPS1 TRUE TRUE FALSE
+SULF2 ARFGEF2 FALSE TRUE FALSE
+NDUFA1 SYNJ2BP:SYNJ2BP-COX16 FALSE TRUE TRUE
+YLPM1 ITPK1 FALSE TRUE FALSE
+LAMP1 MCF2L2 TRUE FALSE TRUE
+PPP1R12A SEPT10 FALSE FALSE TRUE
+CPNE1:NM_001198863:NR_037188 PI3 FALSE FALSE TRUE
+DHX35 ITCH FALSE FALSE TRUE
+NM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8 CEP250 FALSE FALSE TRUE
+RARA PKIA FALSE FALSE TRUE
+STARD3 DOK5:NM_177959 FALSE FALSE TRUE
+NR_036633:VAPB IKZF3:NM_001284514:NM_001284515 FALSE FALSE TRUE
+RAB22A MYO9B FALSE FALSE TRUE
+ACACA STAC2 TRUE TRUE TRUE
+ANKHD1:ANKHD1-EIF4EBP3 PCDH1 FALSE TRUE TRUE

diff -r 8366a8c82a7a -r b21145d59d9c test-data/edgren_test_04_unspecific_matching_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/edgren_test_04_unspecific_matching_output.txt Mon Jan 23 09:41:08 2017 -0500

@@ -0,0 +1,80 @@
+Left-genes Right-genes Spans large gene (>200000bp) edgren_fusion-map.txt edgren_true_positives.txt
+NR_120540 UBA2 FALSE TRUE FALSE
+NR_024091:ZFP91:ZFP91-CNTF LINC00261 FALSE TRUE FALSE
+FAT3 CASC5 TRUE TRUE FALSE
+FAM208B FAM208B FALSE TRUE FALSE
+FRMD4A FRMD4A TRUE TRUE FALSE
+NM_001291876:NM_001291877:TACC2 RPLP1 TRUE TRUE FALSE
+GHITM EEF1A1 FALSE TRUE FALSE
+NM_001286806:NM_001286807:SLC25A30 NDE1 FALSE TRUE FALSE
+YAF2 RYBP FALSE TRUE FALSE
+GALNT6 GALNT6 FALSE TRUE FALSE
+NM_001290002:NM_001290004:NR_120486:NR_120487:ZNF385A NR_120486:NR_120487:ZNF385A FALSE TRUE FALSE
+PUS1 POR FALSE TRUE FALSE
+NM_001159287:TPI1 MLLT6 FALSE TRUE FALSE
+KRT80 NM_001293212:NM_001293213:NM_001293214:NM_001293215:NM_001293216:NR_120608:TUBB FALSE TRUE FALSE
+RPLP0 EEF1A1 FALSE TRUE FALSE
+ZNF609 LY6E FALSE TRUE FALSE
+TEKT4P2 BRWD1 FALSE TRUE FALSE
+AATF HNRNPK FALSE TRUE FALSE
+MRPL38 MAP1LC3A FALSE TRUE FALSE
+MED1 ACSF2:NM_001288968:NM_001288969:NM_001288970:NM_001288971:NM_001288972:NR_110232 FALSE TRUE FALSE
+ARHGAP27:NM_001282290 ARHGAP27:NM_001282290 FALSE TRUE FALSE
+BCAS3 MED13 TRUE TRUE FALSE
+BPTF AMZ2:NM_001289054:NM_001289056 FALSE TRUE FALSE
+CARD14 CARD14 FALSE TRUE FALSE
+RPL26 PDCD2 FALSE TRUE FALSE
+MYH11:NDE1 EIF2A FALSE TRUE FALSE
+VPS35 PPP3R1 FALSE TRUE FALSE
+GATAD2A GATAD2A:NM_001300946 FALSE TRUE FALSE
+PLD3 NM_001291311:PLD3 FALSE TRUE FALSE
+DPY19L3 ARFIP1:NM_001287431:NM_001287432:NM_001287433 FALSE TRUE FALSE
+ZNF317 EEF1A1 FALSE TRUE FALSE
+BCL2L13:NR_073068:NR_073069 NR_031672:SPTAN1 TRUE TRUE FALSE
+HMGN2 ESYT1 FALSE TRUE FALSE
+LOC644961:TMEM222 ACTG1:NR_037688 FALSE TRUE FALSE
+SARS ME2 FALSE TRUE FALSE
+NOS1AP C1orf226 TRUE TRUE FALSE
+KISS1 GOLT1A FALSE TRUE FALSE
+CC2D1B DTYMK FALSE TRUE FALSE
+SYTL1 HSP90AB1 FALSE TRUE FALSE
+PAK2 MAGEA10:MAGEA10-MAGEA5 FALSE TRUE FALSE
+TMCC1 TMCC1 TRUE TRUE FALSE
+HPS3:NM_001308258:NR_046371 CP:NR_046371 FALSE TRUE FALSE
+RSRC1 RSRC1 TRUE TRUE FALSE
+GREB1 GREB1 FALSE TRUE FALSE
+NR_130784 NR_037904:SCLY TRUE TRUE FALSE
+PNKD:TMBIM1 PNKD:TMBIM1 FALSE TRUE FALSE
+PTMA RGL2 FALSE TRUE FALSE
+SLC30A5 AZIN1:NM_001301668 FALSE TRUE FALSE
+NM_001286052:NM_001286053:NM_001286054:NM_001289931:NR_110527:ZNF595:ZNF718 PSPH FALSE TRUE FALSE
+INIP C5 FALSE TRUE FALSE
+RALGPS1 RALGPS1 TRUE TRUE FALSE
+SYNJ2BP:SYNJ2BP-COX16 NDUFA1 FALSE TRUE FALSE
+NEDD8:NEDD8-MDP1 NEDD8:NEDD8-MDP1 FALSE TRUE FALSE
+YLPM1 ITPK1 FALSE TRUE FALSE
+LAMP1 MCF2L2 TRUE FALSE TRUE
+PPP1R12A SEPT10 FALSE FALSE TRUE
+CPNE1:NM_001198863:NR_037188 PI3 FALSE FALSE TRUE
+ITCH DHX35 FALSE FALSE TRUE
+NM_001303457:TTI1 DIDO1 FALSE FALSE TRUE
+NFS1 PREX1 TRUE FALSE TRUE
+CEP250 NM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8 FALSE FALSE TRUE
+SETD3 CCDC85C FALSE FALSE TRUE
+CYTH1 EIF3H FALSE FALSE TRUE
+STARD3 DOK5:NM_177959 FALSE FALSE TRUE
+IKZF3:NM_001284514:NM_001284515 NR_036633:VAPB FALSE FALSE TRUE
+BCAS3 BCAS4 TRUE FALSE TRUE
+SNF8 NM_001272060:RPS6KB1 FALSE FALSE TRUE
+VMP1 NM_001272060:RPS6KB1 FALSE FALSE TRUE
+BSG NFIX FALSE FALSE TRUE
+MYO9B RAB22A FALSE FALSE TRUE
+CMTM7 GLB1 FALSE FALSE TRUE
+NUP214 NOTCH1 FALSE FALSE TRUE
+ZNF704 WDR67 TRUE FALSE TRUE
+SULF2 ARFGEF2 FALSE TRUE TRUE
+RARA PKIA FALSE TRUE TRUE
+GSDMB TATDN1 FALSE TRUE TRUE
+ACACA STAC2 TRUE TRUE TRUE
+MYO19 SKA2 FALSE TRUE TRUE
+ANKHD1:ANKHD1-EIF4EBP3 PCDH1 FALSE TRUE TRUE

diff -r 8366a8c82a7a -r b21145d59d9c tool_dependencies.xml
--- a/tool_dependencies.xml Mon Feb 08 04:56:40 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="python" version="2.7">
-        <repository changeset_revision="8b09fe018cac" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="fuma" version="2.11.0">
-        <repository changeset_revision="58d6b3e8bf1c" name="package_fuma_2_11_3" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>