| Next changeset 1:de66a3316735 (2020-03-02) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2" |
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added:
all_fasta.loc.sample chira_extract.xml macros.xml test-data/alignments.bed test-data/annotation.gtf test-data/chimeras test-data/loci.counts test-data/merged.bed test-data/reads.fasta test-data/reads.fastq test-data/ref.fasta test-data/ref1.fasta test-data/ref2.fasta test-data/segments.bed test-data/singletons tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 0a3107204741 all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Sun Jan 19 16:31:03 2020 -0500 |
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| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
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| diff -r 000000000000 -r 0a3107204741 chira_extract.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chira_extract.xml Sun Jan 19 16:31:03 2020 -0500 |
| [ |
| @@ -0,0 +1,130 @@ +<tool id="chira_extract" name="ChiRA extract" version="@WRAPPER_VERSION@0"> + <description>extrat the chimeras</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ + #set $genomic_fasta = '' + #if str($annotation.annot_choice) == "yes": + #if str($annotation.fasta_source.fasta_source_selector) == 'history': + #set $genomic_fasta = '$annotation.fasta_source.fasta' + #else + #set $genomic_fasta = '$annotation.fasta_source.fasta_id.fields.path' + #end if + #end if + chira_extract.py + -l '$loci' + #if str($annotation.annot_choice) == "yes": + -g '$annotation.gtf' + #if $hybridize: + -f '$genomic_fasta' + #end if + #end if + -tc '$tpm_cutoff' + -sc '$score_cutoff' + -co '$chimeric_overlap' + #if str($reference.ref_type) == "single": + -f1 '$ref_fasta' + #else if str($reference.ref_type) == "split": + -f1 '$ref_fasta1' + -f2 '$ref_fasta2' + #end if + '$hybridize' + -p "\${GALAXY_SLOTS:-2}" + -o ./ + ]]></command> + + <inputs> + <param format="tabular" name="loci" type="data" label="File containing CRLs information"/> + <conditional name="annotation"> + <param name="annot_choice" type="select" label="Have genomic information?" + help="Selecet Yes if you have an annotation file and provide corresponding genomic fasta file"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/> + <conditional name="fasta_source"> + <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file"> + <option value="history" selected="true">History</option> + <option value="preloaded">Server indexed files</option> + </param> + <when value="history"> + <param name="fasta" type="data" format="fasta" label="FASTA file" /> + </when> + <when value="preloaded"> + <param name="fasta_id" type="select"> + <options from_data_table="fasta_indexes" /> + </param> + </when> + </conditional> + </when> + <when value="no"> + <!-- Do nothing --> + </when> + </conditional> + <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1" + help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/> + <param name="score_cutoff" type="float" value="0" label="Score cut-off" min="0" max="2" + help="Hybrids with less than this score will be discarded in the final output. [0-2.0]"/> + <param name="chimeric_overlap" type="integer" value="2" + label=" Maximum number of bases allowed between the chimericsegments of a read"/> + <conditional name="reference"> + <param name="ref_type" type="select" label="Did you use single or split reference for alignment?"> + <option value="split">Split reference</option> + <option value="single">Single reference</option> + </param> + <when value="split"> + <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file" + help="Reference fasta file"/> + <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file" + help="Second reference fasta file."/> + </when> + <when value="single"> + <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file" + help="Reference fasta file"/> + </when> + </conditional> + <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" /> + </inputs> + + <outputs> + <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/> + <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/> + </outputs> + + <tests> + <test expect_num_outputs="2"> + <param name="loci" value="loci.counts"/> + <param name="ref_type" value="split"/> + <param name="ref_fasta1" value="ref1.fasta"/> + <param name="ref_fasta2" value="ref2.fasta"/> + <param name="annot_choice" value="no"/> + <param name="hybridize" value="true" /> + <output name="chimeras" file="chimeras" sort="True"/> + <output name="singletons" file="singletons" sort="True"/> + </test> + </tests> + <help> + +.. class:: infomark + +**What it does** + +This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to. + +**Inputs** + + * Tabular file containing CRLs information + * Annotation GTF file + * Reference fasta files. Provide both in case of split reference. + * If your alignments are merged at genomic level in previous step (chira merge), then provide a reference genomic fasta fille. + +**Output** + + * Tabular file containing chimeras information + </help> + <expand macro="citations" /> +</tool> + |
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| diff -r 000000000000 -r 0a3107204741 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Jan 19 16:31:03 2020 -0500 |
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| @@ -0,0 +1,15 @@ +<macros> + <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token> + <token name="@TOOL_VERSION@">1.0.2</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">chira</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <yield /> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 0a3107204741 test-data/alignments.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignments.bed Sun Jan 19 16:31:03 2020 -0500 |
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| b'@@ -0,0 +1,337 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| diff -r 000000000000 -r 0a3107204741 test-data/annotation.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotation.gtf Sun Jan 19 16:31:03 2020 -0500 |
| b |
| b'@@ -0,0 +1,58 @@\n+14\t.\tmiRNA\t115044183\t115044205\t.\t+\t.\tID=MIMAT0000529;Alias=MIMAT0000529;Name=mmu-miR-20a-5p;Derives_from=MI0000568\n+16\t.\tmiRNA\t93369775\t93369796\t.\t+\t.\tID=MIMAT0017240;Alias=MIMAT0017240;Name=mmu-miR-802-3p;Derives_from=MI0004249\n+1\t.\tmiRNA\t36348732\t36348753\t.\t-\t.\tID=MIMAT0027696;Alias=MIMAT0027696;Name=mmu-miR-6898-5p;Derives_from=MI0022745\n+18\t.\tmiRNA\t37854605\t37854625\t.\t-\t.\tID=MIMAT0027861;Alias=MIMAT0027861;Name=mmu-miR-6979-3p;Derives_from=MI0022827\n+11\thavana\ttranscript\t116338339\t116347444\t.\t-\t.\tgene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; transcript_support_level "3";\n+11\thavana\texon\t116347342\t116347444\t.\t-\t.\tgene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "1"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00000834936"; exon_version "1"; transcript_support_level "3";\n+11\thavana\texon\t116347033\t116347098\t.\t-\t.\tgene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "2"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001212609"; exon_version "1"; transcript_support_level "3";\n+11\thavana\texon\t116345907\t116345955\t.\t-\t.\tgene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "3"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001217820"; exon_version "1"; transcript_support_level "3";\n+11\thavana\texon\t116340338\t116340378\t.\t-\t.\tgene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "4"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001233021"; exon_version "1"; transcript_support_level "3";\n+11\thavana\texon\t116338339\t116338830\t.\t-\t.\tgene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "5"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00000796470"; exon_version "1"; transcript_support_level "3";\n+2\thavana\ttranscript\t128237693\t128239643\t.\t-\t.\tgene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "1";\n+2\thavana\texon\t128239424\t128239643\t.\t-\t.\tgene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; exon_number "1"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSMUSE00000756585"; exon_version "1"; tag "basic"; transcript_support_level "1";\n+2\thavana\texon\t128238858\t128239058\t.\t-\t.\tgene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; exon_number "2"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_nam'..b'_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\texon\t27707880\t27708067\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "9"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000459997"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\tCDS\t27707880\t27708067\t.\t+\t1\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "9"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\texon\t27708426\t27711106\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "10"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000348638"; exon_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\tCDS\t27708426\t27708532\t.\t+\t2\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "10"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\tstop_codon\t27708533\t27708535\t.\t+\t0\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "10"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\tUTR\t27655588\t27655759\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\tUTR\t27701767\t27701887\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\tUTR\t27708536\t27711106\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n' |
| b |
| diff -r 000000000000 -r 0a3107204741 test-data/chimeras --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chimeras Sun Jan 19 16:31:03 2020 -0500 |
| b |
| @@ -0,0 +1,3 @@ +tagid txid1 txid2 geneid1 geneid2 symbol1 symbol2 region1 region2 tx_pos_start1 tx_pos_end1 tx_pos_strand1 length1 tx_pos_start2 tx_pos_end2 tx_pos_strand2 length2 read_info genomic_pos1 genomic_pos2 locus1 locus2 groupid1 groupid2 tpm1 tpm2 score1 score2 score sequences hybrid hybrid_pos mfe +4|1 ENSMUST00000136025 mmu-miR-6979-3p NA NA NA NA NA NA 32 46 + NA 2 12 + NA 2,15,30,39,54 ENSMUST00000136025:32:46:+ mmu-miR-6979-3p:2:12:+ ENSMUST00000136025:32:46:+ mmu-miR-6979-3p:2:12:+ 1 7 121100.0 165100.0 1.0 1.0 2.0 CAGGACUCUUGGCU&GUGUCUGUCU NA NA NA +3|2 mmu-miR-20a-5p ENSMUST00000136025 NA NA NA NA NA NA 0 23 + NA 132 142 + NA 6,28,35,44,55 mmu-miR-20a-5p:0:23:+ ENSMUST00000136025:132:142:+ mmu-miR-20a-5p:0:23:+ ENSMUST00000136025:132:142:+ 5 2 75660.0 165100.0 1.0 1.0 2.0 UAAAGUGCUUAUAGUGCAGGUAG&CUGCCUGCCU ((.((((((((&)))))))))) 13&1 -10.88 |
| b |
| diff -r 000000000000 -r 0a3107204741 test-data/loci.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/loci.counts Sun Jan 19 16:31:03 2020 -0500 |
| b |
| @@ -0,0 +1,9 @@ +6|1|1 ENSMUST00000182010 4 0 19 68 + 5S49M1S ENSMUST00000182010:19:68:+ ENSMUST00000182010:19:74:+ 1 1 6.485e+04 +7|9|1 ENSMUST00000182010 4 0 24 74 + 5S50M ENSMUST00000182010:24:74:+ ENSMUST00000182010:19:74:+ 1 1 6.485e+04 +4|1|2 ENSMUST00000136025 0 1 32 46 + 1S14M39S ENSMUST00000136025:32:46:+ ENSMUST00000136025:32:46:+ 1 1 1.211e+05 +3|2|2 ENSMUST00000136025 1 2 132 142 + 34S10M11S ENSMUST00000136025:132:142:+ ENSMUST00000136025:132:142:+ 1 1 1.651e+05 +2|2|2 ENSMUST00000137264 2 3 12 27 + 4S15M30S ENSMUST00000137264:12:27:+ ENSMUST00000137264:12:27:+ 1 1 1.135e+05 +6|1|4 ENSMUST00000160533 3 4 69 82 + 42S13M ENSMUST00000160533:69:82:+ ENSMUST00000160533:69:82:+ 1 1 1.297e+05 +3|2|1 mmu-miR-20a-5p 5 5 0 23 + 5S23M27S mmu-miR-20a-5p:0:23:+ mmu-miR-20a-5p:0:23:+ 1 1 7.566e+04 +2|2|1 mmu-miR-6898-5p 6 6 11 21 + 10M39S mmu-miR-6898-5p:11:21:+ mmu-miR-6898-5p:11:21:+ 1 1 1.651e+05 +4|1|1 mmu-miR-6979-3p 7 7 2 12 + 29S10M15S mmu-miR-6979-3p:2:12:+ mmu-miR-6979-3p:2:12:+ 1 1 1.651e+05 |
| b |
| diff -r 000000000000 -r 0a3107204741 test-data/merged.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged.bed Sun Jan 19 16:31:03 2020 -0500 |
| b |
| @@ -0,0 +1,8 @@ +ENSMUST00000136025 32 46 + 4|1|2,ENSMUST00000136025,32,46,+,1S14M39S +ENSMUST00000136025 132 142 + 3|2|2,ENSMUST00000136025,132,142,+,34S10M11S +ENSMUST00000137264 12 27 + 2|2|2,ENSMUST00000137264,12,27,+,4S15M30S +ENSMUST00000160533 69 82 + 6|1|4,ENSMUST00000160533,69,82,+,42S13M +ENSMUST00000182010 19 74 + 6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M +mmu-miR-20a-5p 0 23 + 3|2|1,mmu-miR-20a-5p,0,23,+,5S23M27S +mmu-miR-6898-5p 11 21 + 2|2|1,mmu-miR-6898-5p,11,21,+,10M39S +mmu-miR-6979-3p 2 12 + 4|1|1,mmu-miR-6979-3p,2,12,+,29S10M15S |
| b |
| diff -r 000000000000 -r 0a3107204741 test-data/reads.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fasta Sun Jan 19 16:31:03 2020 -0500 |
| b |
| @@ -0,0 +1,14 @@ +>1|1 +AAAAGACTCTGTAGACATGGCTGGTCTTGAACTCACAGAGATTTGTCTGCCTTTC +>2|2 +ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA +>3|2 +CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA +>4|1 +TCAGGACTCTTGGCTGTATCCTTTCCTAAGTGTCTGTCTTCCTTACCACTAACA +>5|8 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA +>6|1 +TGTGGTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATTAGATACCGTC +>7|9 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT |
| b |
| diff -r 000000000000 -r 0a3107204741 test-data/reads.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fastq Sun Jan 19 16:31:03 2020 -0500 |
| b |
| @@ -0,0 +1,96 @@ +@183438/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG +@397634/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHGHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG +@701890/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +EEGGHGHHHHHHHHHGGGGGGHGGCGGFGHGHHGGHGGGHGHHHHHHGGGGGGFG +@745414/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGF +@753363/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +EEEGHHHFHHHHHHHGGFEEFGGGGGGGHHGHHGGHGGFHGHHHHHHGFGGGGGG +@881071/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGFGGGHHGHHGGHGGGHGHHHHHHGFGGFHGG +@1059959/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGEHHGHHGGHGGGHGHHHHHHGGGGGHGG +@1157152/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGEHHGHHGGHGGGHGHHHHHHGGGGGHGG +@1295751/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG +@585749/1 +TGTGGTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATTAGATACCGTC ++ +GGEGGHHHHHHHHHHHFHHHG?FGEHHGGGFEEHHGHHGGFF?FHGHHHHHGEGG +@1209323/1 +ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA ++ +3AAABFFBBBBBGGEFGGG2AAGHHGGAGHHHHHHHHCHGHHHHHH5GF +@1248864/1 +ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA ++ +ABBBAF4DAB?BGGEFEFG2AAF3CEGGHHGGFCG33FHFHFHHHHHHH +@475998/1 +CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA ++ +GGEEGB1FFFDGGGFHHHDDFGGHFHEFHHHHFDGGGE?GHFHHHHFHHHDEDHD +@478112/1 +CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA ++ +EEFGGFGEHHFGHBBFHHHFGHHHHAGHHHFHFFGEF@BFGGAEHFFHHHGHGHF +@74093/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +G?FHHFFHFEFHH3FBAGGC2AAFEEGHFGFDEGGGFEAGFGE5AFF5@@BE5G +@448633/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +EFGGFHH5BAFA23AAFFHHDGGHHFGHHHEGHCFGFAFGH3FGGBBG@E@FGF +@849624/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +AABFBFFFF2CGDBADEFB2FAFFFHBGHFHDFGHAEGCFFEFDD5GGG@BBFE +@1076923/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +GCEFGHHHFEFH23DB553A2BGFFDBBA35FGFFGGGEECGH5DD@@@EBEGF +@1278542/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +EGGFHGHHHHGHGEGFHHHHHHFHHHFHGFGHHHHHGGEE3GHGGHGFDBGHHE +@1290525/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +CEFFDHH5B2AE2F555532AGF3EGH3AFAEHHFHGD133335DFGH5D@3FF +@1379287/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +AEEF1FGHHHGHHFGHHHGG/E1EHHHHGHHFDGGEG?CFGBGEGHHGHHHHHH +@1490590/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +GEA3BD5DF2EGCGEDF5EGH3AGHHHFHGFBFHBGGGGH33BFFD555D53FG +@854752/1 +AAAAGACTCTGTAGACATGGCTGGTCTTGAACTCACAGAGATTTGTCTGCCTTTC ++ +G?EFFAF5335DD5B5553222B1A55AFAGHHE33BAF325555A5DF5B3F3B +@1180232/1 +TCAGGACTCTTGGCTGTATCCTTTCCTAAGTGTCTGTCTTCCTTACCACTAACA ++ +EGE0F10B01DDBGC/0BFFGGHHHFE21BA2D221DGHH2DBAGHBDFBG1GF |
| b |
| diff -r 000000000000 -r 0a3107204741 test-data/ref.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref.fasta Sun Jan 19 16:31:03 2020 -0500 |
| b |
| @@ -0,0 +1,18 @@ +>mmu-miR-20a-5p +TAAAGTGCTTATAGTGCAGGTAG +>mmu-miR-802-3p +ACGGAGAGTCTTTGTCACTCAG +>mmu-miR-6898-5p +TGTAAGGGGAGATGCAGGGAGC +>mmu-miR-6979-3p +TTGTGTCTGTCTGGCTCCCAG +>ENSMUST00000137264 +CTACTCACATGAAGGGAGGACGATGCGCAACCCTCCACCCACCTGCCTCATCGCCTGTAACCGCGATTCTTACCCTCTCAGAAAGAACCAGAAGCCTTCCCTCTGTGGGCTAATACGTGCCAGCCAAACCTGTGGGCCAGCTGAGCTGAGGGTCAGGGCTGGTTGTTTCTGTAGGCTTTCTCTTCTGAGTGGAGACCAAGAAGACTGAAGAGTTTGGCAGCCTTGTTAGACGCCCATGGACAGGTTTTGGTCTCTGGCACTC +>ENSMUST00000136025 +GATCTGATTGAGTCACAGCTGAGATGTGGCACCAGGACTCTTGGCTACACTCAGTTCTCTCAGTTTGACTGAGTACTCTGGGATCACAGAAGTGACTACATGATGCAGCCCAGAGGTCTGAACTCAAAGCTTCTGCCTGCCTACCTTATCTCACTGCTGGCAAATGCATCCCCTCTGCTCCACCCATC +>ENSMUST00000182010 +GCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGTTTCGAAGACGATCAGATACCGTTGTAGTTCCAACCATAAACGATGCCGACTGGC +>ENSMUST00000160533 +CAAAGGCAGTATCGTGGTGGATTATGATGTCATCCTGAAGGCCAAGTACACCCCAGGATTTGAAAACACATTAGATACCGTCGTCAAAAACCTGGAGACA +>ENSMUST00000045896 +GAGGCCAATGGTGGCGCCAACCCCTTCGAGGATGATGCCAAGGGAGTTCGTGTACGGGCACTCTATGACTACGACGGTCAGGAGCAGGATGAGCTCAGCT |
| b |
| diff -r 000000000000 -r 0a3107204741 test-data/ref1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref1.fasta Sun Jan 19 16:31:03 2020 -0500 |
| b |
| @@ -0,0 +1,8 @@ +>mmu-miR-20a-5p +TAAAGTGCTTATAGTGCAGGTAG +>mmu-miR-802-3p +ACGGAGAGTCTTTGTCACTCAG +>mmu-miR-6898-5p +TGTAAGGGGAGATGCAGGGAGC +>mmu-miR-6979-3p +TTGTGTCTGTCTGGCTCCCAG |
| b |
| diff -r 000000000000 -r 0a3107204741 test-data/ref2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref2.fasta Sun Jan 19 16:31:03 2020 -0500 |
| b |
| @@ -0,0 +1,10 @@ +>ENSMUST00000137264 +CTACTCACATGAAGGGAGGACGATGCGCAACCCTCCACCCACCTGCCTCATCGCCTGTAACCGCGATTCTTACCCTCTCAGAAAGAACCAGAAGCCTTCCCTCTGTGGGCTAATACGTGCCAGCCAAACCTGTGGGCCAGCTGAGCTGAGGGTCAGGGCTGGTTGTTTCTGTAGGCTTTCTCTTCTGAGTGGAGACCAAGAAGACTGAAGAGTTTGGCAGCCTTGTTAGACGCCCATGGACAGGTTTTGGTCTCTGGCACTC +>ENSMUST00000136025 +GATCTGATTGAGTCACAGCTGAGATGTGGCACCAGGACTCTTGGCTACACTCAGTTCTCTCAGTTTGACTGAGTACTCTGGGATCACAGAAGTGACTACATGATGCAGCCCAGAGGTCTGAACTCAAAGCTTCTGCCTGCCTACCTTATCTCACTGCTGGCAAATGCATCCCCTCTGCTCCACCCATC +>ENSMUST00000182010 +GCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGTTTCGAAGACGATCAGATACCGTTGTAGTTCCAACCATAAACGATGCCGACTGGC +>ENSMUST00000160533 +CAAAGGCAGTATCGTGGTGGATTATGATGTCATCCTGAAGGCCAAGTACACCCCAGGATTTGAAAACACATTAGATACCGTCGTCAAAAACCTGGAGACA +>ENSMUST00000045896 +GAGGCCAATGGTGGCGCCAACCCCTTCGAGGATGATGCCAAGGGAGTTCGTGTACGGGCACTCTATGACTACGACGGTCAGGAGCAGGATGAGCTCAGCT |
| b |
| diff -r 000000000000 -r 0a3107204741 test-data/segments.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/segments.bed Sun Jan 19 16:31:03 2020 -0500 |
| b |
| @@ -0,0 +1,13 @@ +ENSMUST00000182010 19 68 6|1|1,ENSMUST00000182010,19,68,+,5S49M1S 0 + +ENSMUST00000182010 24 74 7|9|1,ENSMUST00000182010,24,74,+,5S50M 0 + +mmu-miR-20a-5p 0 23 3|2|1,mmu-miR-20a-5p,0,23,+,5S23M27S 0 + +mmu-miR-6898-5p 11 21 2|2|1,mmu-miR-6898-5p,11,21,+,10M39S 0 + +mmu-miR-6979-3p 2 12 4|1|1,mmu-miR-6979-3p,2,12,+,29S10M15S 0 + +ENSMUST00000137264 12 27 2|2|2,ENSMUST00000137264,12,27,+,4S15M30S 0 + +ENSMUST00000136025 32 46 4|1|2,ENSMUST00000136025,32,46,+,1S14M39S 0 + +ENSMUST00000136025 132 142 3|2|2,ENSMUST00000136025,132,142,+,34S10M11S 0 + +ENSMUST00000182010 19 45 6|1|2,ENSMUST00000182010,19,45,+,5S26M24S 0 + +ENSMUST00000182010 24 45 7|9|2,ENSMUST00000182010,24,45,+,5S21M29S 0 + +ENSMUST00000182010 46 58 6|1|3,ENSMUST00000182010,46,58,+,32S12M11S 0 + +ENSMUST00000182010 46 68 7|9|3,ENSMUST00000182010,46,68,+,27S22M6S 0 + +ENSMUST00000160533 69 82 6|1|4,ENSMUST00000160533,69,82,+,42S13M 0 + |
| b |
| diff -r 000000000000 -r 0a3107204741 test-data/singletons --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/singletons Sun Jan 19 16:31:03 2020 -0500 |
| b |
| @@ -0,0 +1,4 @@ +tagid txid geneid symbol region tx_pos_start tx_pos_end tx_pos_strand length read_info genomic_pos locus groupid tpm score score sequences +6|1 ENSMUST00000182010 NA NA NA 19 68 + NA 6,54,55 ENSMUST00000182010:19:68:+ ENSMUST00000182010:19:74:+ 0 64850.0 1.0 1.0 UCAUUAAUCAAGAACGAAAGUCGGAGUUUCGAAGACGAUCAGAUACCGUUGUAGU +7|9 ENSMUST00000182010 NA NA NA 24 74 + NA 6,55,55 ENSMUST00000182010:24:74:+ ENSMUST00000182010:19:74:+ 0 64850.0 1.0 1.0 UCAUUAAUCAAGAACGAAAGUCGGAGUUUCGAAGACGAUCAGAUACCGUUGUAGU +2|2 ENSMUST00000137264 NA NA NA 12 27 + NA 5,19,49 ENSMUST00000137264:12:27:+ ENSMUST00000137264:12:27:+ 3 113500.0 1.0 1.0 AGGGAGGACGAUGCG |
| b |
| diff -r 000000000000 -r 0a3107204741 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Jan 19 16:31:03 2020 -0500 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="all_fasta.loc" /> + </table> +</tables> |