| Next changeset 1:40dc77f3730c (2015-02-04) |
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Commit message:
Imported from capsule None |
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added:
quantifier.xml test-data/expression_galaxy.html test-data/mature_ref_this_species.fa test-data/miRNAs_expressed_all_samples.csv test-data/precursors_ref_this_species.fa test-data/reads_collapsed.fa tool_dependencies.xml |
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| diff -r 000000000000 -r 2c039fc73f1f quantifier.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/quantifier.xml Tue Jan 27 09:06:15 2015 -0500 |
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| @@ -0,0 +1,145 @@ +<tool id="rbc_mirdeep2_quantifier" name="MiRDeep2 Quantifier" version="2.0.0"> + <description> +<![CDATA[ +fast quantitation of reads mapping to known miRBase precursors +]]> + </description> + <requirements> + <requirement type="package" version="2.0">mirdeep2_quantifier</requirement> + <requirement type="package" version="0.12.7">bowtie</requirement> + <requirement type="package" version="5.18.1">perl</requirement> + <requirement type="package" version="1.8.5">vienna_rna</requirement> + <requirement type="package" version="2.023">pdf_api2</requirement> + </requirements> + + <command> +<![CDATA[ + quantifier.pl + + -p $precursors + + -m $mature + + -r $reads + + #if $species.value != 'all' + -t $species + #end if + + #if $star_sequences + -s $star_sequences + #end if + + $sortReadsInPDF + $flexibleIdMapping + $skipFileConversion + $wholePrecursAsMature + $discardReadMultiMap + + -e $upstreamNtides + -f $downstreamNtides + -g $allowedMismatches + -y galaxy + + ## html output + ; + cp expression_galaxy.html $html 2> /dev/null + + ## move pdf directory to be accessible from the new index.html + ; + mkdir -p $html.files_path 2> /dev/null + ; + cp -R pdfs_galaxy $html.files_path 2> /dev/null + +]]> + </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + <inputs> + <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads" help="Reads in fasta format. (-r)"/> + <param name="precursors" format="fasta" type="data" label="Precursor sequences" help="miRNA precursor sequences from miRBase. (-p)"/> + <param name="mature" format="fasta" type="data" label="Mature miRNA sequences" help="Mature miRNA sequences from miRBase. (-m)"/> + <param name="species" type="select" label="Search in species" help="If not searching in a specific species all species in your files will be analyzed. (-t)"> + <option value="all">All species</option> + <option value="tni">tetraodon</option> + <option value="dps">d.pseudoobscura</option> + <option value="dya">d.yakuba</option> + <option value="ame">a.mellifera</option> + <option value="dmo">d.mojavensis</option> + <option value="cel">worm</option> + <option value="aga">a.gambiae</option> + <option value="cbr">c.briggsae</option> + <option value="cin">c.intestinalis</option> + <option value="mmu">mouse</option> + <option value="xtr">x.tropicalis</option> + <option value="eca">horse</option> + <option value="cfa">dog</option> + <option value="fru">fugu</option> + <option value="bta">cow</option> + <option value="der">d.erecta</option> + <option value="dgr">d.grimshawi</option> + <option value="gga">chicken</option> + <option value="spu">s.purpuratus</option> + <option value="bfl">lancelet</option> + <option value="ptr">chimp</option> + <option value="dse">d.sechellia</option> + <option value="dpe">d.persimilis</option> + <option value="dvi">d.virilis</option> + <option value="rno">rat</option> + <option value="dme">d.melanogaster</option> + <option value="lca">cat</option> + <option value="sja">c.japonica</option> + <option value="dan">d.ananassae</option> + <option value="hsa">human</option> + <option value="dsi">d.simulans</option> + </param> + <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/> + + <!-- <param name="generatePDFs" type="boolean" checked="true" truevalue="" falsevalue="-d" label="Generate PDFs" help="(-d)"/> --> + <param name="sortReadsInPDF" type="boolean" checked="true" truevalue="" falsevalue="-o" label="Sort reads by sample in PDF" help="(-o)"/> + <param name="flexibleIdMapping" type="boolean" checked="false" truevalue="-k" falsevalue="" label="Include ID-flexible mapping" help="Also considers precursor-mature mappings that have different ids, eg let7c would be allowed to map to pre-let7a. (-k)"/> + <param name="skipFileConversion" type="boolean" checked="false" truevalue="-n" falsevalue="" label="Skip file conversion" help="(-n)"/> + <param name="skipPrecursMapping" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Skip mapping against precursor" help="(-x)"/> + <!-- <param name="noMrdPDF" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Do not create output.mrd file or PDFs" help="(-j)"/> --> + <param name="wholePrecursAsMature" type="boolean" checked="false" truevalue="-w" falsevalue="" label="Consider the whole precursor as the 'mature sequence'" help="(-w)"/> + <param name="discardReadMultiMap" type="boolean" checked="false" truevalue="-U" falsevalue="" label="Discard all read multimapper" help="(-U)"/> + + <param name="upstreamNtides" type="integer" value="2" minvalue="0" label="Upstream nucleotides" help="Number of nucleotides upstream of the mature sequence to consider. (-e)"/> + <param name="downstreamNtides" type="integer" value="5" minvalue="0" label="Downstream nucleotides" help="Number of nucleotides downstream of the mature sequence to consider. (-f)"/> + <param name="allowedMismatches" type="integer" value="1" minvalue="0" label="Allowed mismatches" help="Number of allowed mismatches when mapping reads to precursors. (-g)"/> + </inputs> + <outputs> + <data name="miRNAsExpressed" format="tabular" from_work_dir="miRNAs_expressed_all_samples_galaxy.csv" label="output of ${tool.name} on ${on_string}"/> + <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"/> + </outputs> + <tests> + <test> + <param name="reads" value="reads_collapsed.fa"/> + <param name="precursors" value="precursors_ref_this_species.fa"/> + <param name="mature" value="mature_ref_this_species.fa"/> + <param name="species" value="cel"/> + <output name="miRNAsExpressed" file="miRNAs_expressed_all_samples.csv"/> + <output name="html" file="expression_galaxy.html"/> + </test> + </tests> + <help> +<![CDATA[ +**What MiRDeep2 Quantifier does** + +The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. +First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. +By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. +The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined. +]]> + </help> + <citations> + <citation type="doi">10.1093/nar/gkr688</citation> + <citation type="doi">10.1002/0471250953.bi1210s36</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 2c039fc73f1f test-data/expression_galaxy.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/expression_galaxy.html Tue Jan 27 09:06:15 2015 -0500 |
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| b'@@ -0,0 +1,374 @@\n+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"\n+ "http://www.w3.org/TR/html4/strict.dtd">\n+ <html>\n+ <head>\n+ <title>miRDeep2</title>\n+ <!-- CSS code -->\n+ <style type="text/css">\n+ body{\n+ font: .75em Arial,sans-serif; \n+ background: #FFFFFF; \n+ color: #333333\n+ }\n+div#\n+container\n+{\n+ width: 1000px; \n+ margin:0 auto\n+ }\n+h1{ \n+ color: #F60; \n+ margin: 1em 0 0; \n+ letter-spacing: -2px; \n+}\n+p{\n+ margin: 0 0 1.7em; \n+}\n+\n+a.tooltip{\n+\ttext-decoration:none;\n+\tcolor:black;\n+ font-weight:bold;\n+}\n+\n+a.tooltip:hover\n+{ position: relative; \n+ background: transparent; \n+\t\n+} \n+\n+a.tooltip span \n+{ position: absolute; \n+ visibility: hidden; \n+\n+ width: 20em; \n+ top: 1.5em; \n+ background: #ffffdd; \n+}\n+\n+a.tooltip:hover span \n+{ visibility: visible; }\n+\n+\n+a.tooltip2{\n+\ttext-decoration:none;\n+\tcolor:black;\n+ font-weight:bold;\n+}\n+\n+a.tooltip2:hover\n+{ position: relative; \n+ background: transparent; \n+\t\n+} \n+\n+a.tooltip2 span \n+{ position: absolute; \n+ visibility: hidden; \n+\n+ width: 20em; \n+ top: 1.5em;left:-10em; \n+ background: #ffffdd; \n+}\n+\n+a.tooltip2:hover span \n+{ visibility: visible; }\n+\n+\n+a.tooltip3{\n+\ttext-decoration:none;\n+\tcolor:black;\n+ font-weight:bold;\n+}\n+\n+a.tooltip3:hover\n+{ position: relative; \n+ background: transparent; \n+\t\n+} \n+\n+a.tooltip3 span \n+{ position: absolute; \n+ visibility: hidden; \n+\n+ width: 20em; \n+ top: 3em; \n+ background: #ffffdd; \n+}\n+\n+a.tooltip3:hover span \n+{ visibility: visible; }\n+\n+\n+a.tooltip4{\n+\ttext-decoration:none;\n+\tcolor:black;\n+ font-weight:bold;\n+}\n+\n+a.tooltip4:hover\n+{ position: relative; \n+ background: transparent; \n+\t\n+} \n+\n+a.tooltip4 span \n+{ position: absolute; \n+ visibility: hidden; \n+\n+ width: 20em; \n+ top:3em;left:-10em; \n+ background: #ffffdd; \n+}\n+\n+a.tooltip4:hover span \n+{ visibility: visible; }\n+\n+\n+\n+</style>\n+ \n+ </head>\n+ <body>\n+ <table border="0" width="100%">\n+ <colgroup>\n+ <col width="5*">\n+ <col width="5*">\n+ </colgroup>\n+ <tr height="200" valign="top">\n+ <td><font face="Times New Roman" size="8">\n+ <b><a href="http://www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/index.html" target="_blank" style="color:Black;text-decoration:none" title="miRDeep2 homepage at MDC-Berlin" >miRDeep2</a></b>\n+ \n+ \n+ <br>\n+ <br>\n+ </font></td>\n+ <td> <a href="http://www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/index.html" target="_blank" >\n+ <img src="http://www.mdc-berlin.de/de/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/mirdeep.jpg" style="border-style: none" name="precursor miRNA" title="miRDeep2 homepage at MDC-Berlin" align=right alt="miRDeep home"/></a></td>\n+ </tr>\n+ </table>\n+ \n+<br>\n+ <br>\n+ <br><h2></h2><br>\n+ <font face="Times New Roman" size="2">\n+ <table border="1">\n+<th><a href="" class="tooltip3">miRBase precursor id<span>Clicking this field will display a pdf of the structure and read signature of the miRNA.</span></a></th>\n+\n+<th><a href="" class="tooltip3">total read count<span>this is the sum of read counts for the mature and star miRNAs.</span></a></th>\n+\n+<th><a href="" class="tooltip3">mature read count(s)<span>this is the number of reads that map to the miRNA hairpin and are contained in the '..b'eotide&SUBJECTS_FROM=&SUBJECTS_TO=&SUBJECTFILE=&DBTYPE=gc&DATABASE=nr&EQ_MENU=&NUM_ORG=1&EQ_TEXT=&BLAST_PROGRAMS=blastn&PHI_PATTERN=&MAX_NUM_SEQ=100&SHORT_QUERY_ADJUST=on&EXPECT=10&WORD_SIZE=7&MATRIX_NAME=PAM30&MATCH_SCORES=2,-3&GAPCOSTS=5+2&COMPOSITION_BASED_STATISTICS=0&FILTER=L&REPEATS=repeat_9606&FILTER=m&TEMPLATE_LENGTH=0&TEMPLATE_TYPE=0&PSSM=&I_THRESH=&SHOW_OVERVIEW=true&SHOW_LINKOUT=true&GET_SEQUENCE=auauauaauauauauauauuauaa&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&ALIGNMENT_VIEW=Pairwise&MASK_CHAR=2&MASK_COLOR=1&DESCRIPTIONS=100&ALIGNMENTS=100&NEW_VIEW=true&OLD_BLAST=false&NCBI_GI=false&SHOW_CDS_FEATURE=false&NUM_OVERVIEW=100&FORMAT_EQ_TEXT=&FORMAT_ORGANISM=&EXPECT_LOW=&EXPECT_HIGH=&QUERY_INDEX=&CLIENT=web&SERVICE=plain&CMD=request&PAGE=Nucleotides&PROGRAM=blastn&MEGABLAST=&RUN_PSIBLAST=&TWO_HITS=&DEFAULT_PROG=megaBlast&WWW_BLAST_TYPE=&DB_ABBR=&SAVED_PSSM=&SELECTED_PROG_TYPE=blastn&SAVED_SEARCH=true&BLAST_SPEC=&QUERY_BELIEVE_DEFLINE=&DB_DIR_PREFIX=&USER_DATABASE=&USER_WORD_SIZE=&USER_MATCH_SCORES=&USER_FORMAT_DEFAULTS=&NO_COMMON=&NUM_DIFFS=2&NUM_OPTS_DIFFS=1&UNIQ_DEFAULTS_NAME=A_SearchDefaults_1Mn7ZD_2Sq4_1Z58HQ5Jb_23tpbD_167y9p&PAGE_TYPE=BlastSearch&USER_DEFAULT_PROG_TYPE=blastn&USER_DEFAULT_MATCH_SCORES=3. target="_blank">blast</a></td>\n+ <td><table><tr><td>ucaccgggagaaaaacuggagu</td></tr></table></td>\n+<td><table><tr><td>-</td></tr></table></td>\n+<td>ucugugagccagguccuguuccgguuuuuuccguggugauaacgcauccaaaagucucuaucaccgggagaaaaacuggaguaggaccugugacucau</td>\n+\t\t\t</tr> \n+<tr><td nowrap="nowrap"><a href="pdfs_galaxy/cel-mir-41.pdf">cel-mir-41</a></td>\n+ <td>164</td> \n+ <td>\n+\n+\n+<table><tr><td WIDTH=55>id</td><td>seq</td><td>seq(norm)</td>\n+<tr><td nowrap="nowrap"><a href="http://www.mirbase.org/cgi-bin/query.pl?terms=cel-mir-41" target="_blank">cel-miR-41</a></td><td><nobr>87.00</nobr></td><td><nobr>498.01</nobr></td></tr>\n+</table>\n+\n+</td>\n+\n+\n+<td>\n+<table><tr><td WIDTH=55>id</td><td>seq</td><td>seq(norm)</td>\n+<tr><td nowrap="nowrap"><a>na</a></td><td><nobr>0</nobr></td><td><nobr>0</nobr></td></tr>\n+</table>\n+\n+</td>\n+\n+\n+ \n+\t\t\t<td nowrap="nowrap">77</td>\n+ <td> - </td>\n+ <td><a href=http://blast.ncbi.nlm.nih.gov/Blast.cgi?QUERY=gggucccagagaccuuggugguuuuucucugcagugauagauacuucuaacaacucgcuaucaccgggugaaaaaucaccuaggucuggagccuccu&JOB_TITLE=cel-mir-41&db=nucleotide&QUERY_FROM=&QUERY_TO=&QUERYFILE=&GENETIC_CODE=1&SUBJECTS=&stype=nucleotide&SUBJECTS_FROM=&SUBJECTS_TO=&SUBJECTFILE=&DBTYPE=gc&DATABASE=nr&EQ_MENU=&NUM_ORG=1&EQ_TEXT=&BLAST_PROGRAMS=blastn&PHI_PATTERN=&MAX_NUM_SEQ=100&SHORT_QUERY_ADJUST=on&EXPECT=10&WORD_SIZE=7&MATRIX_NAME=PAM30&MATCH_SCORES=2,-3&GAPCOSTS=5+2&COMPOSITION_BASED_STATISTICS=0&FILTER=L&REPEATS=repeat_9606&FILTER=m&TEMPLATE_LENGTH=0&TEMPLATE_TYPE=0&PSSM=&I_THRESH=&SHOW_OVERVIEW=true&SHOW_LINKOUT=true&GET_SEQUENCE=auauauaauauauauauauuauaa&FORMAT_OBJECT=Alignment&FORMAT_TYPE=HTML&ALIGNMENT_VIEW=Pairwise&MASK_CHAR=2&MASK_COLOR=1&DESCRIPTIONS=100&ALIGNMENTS=100&NEW_VIEW=true&OLD_BLAST=false&NCBI_GI=false&SHOW_CDS_FEATURE=false&NUM_OVERVIEW=100&FORMAT_EQ_TEXT=&FORMAT_ORGANISM=&EXPECT_LOW=&EXPECT_HIGH=&QUERY_INDEX=&CLIENT=web&SERVICE=plain&CMD=request&PAGE=Nucleotides&PROGRAM=blastn&MEGABLAST=&RUN_PSIBLAST=&TWO_HITS=&DEFAULT_PROG=megaBlast&WWW_BLAST_TYPE=&DB_ABBR=&SAVED_PSSM=&SELECTED_PROG_TYPE=blastn&SAVED_SEARCH=true&BLAST_SPEC=&QUERY_BELIEVE_DEFLINE=&DB_DIR_PREFIX=&USER_DATABASE=&USER_WORD_SIZE=&USER_MATCH_SCORES=&USER_FORMAT_DEFAULTS=&NO_COMMON=&NUM_DIFFS=2&NUM_OPTS_DIFFS=1&UNIQ_DEFAULTS_NAME=A_SearchDefaults_1Mn7ZD_2Sq4_1Z58HQ5Jb_23tpbD_167y9p&PAGE_TYPE=BlastSearch&USER_DEFAULT_PROG_TYPE=blastn&USER_DEFAULT_MATCH_SCORES=3. target="_blank">blast</a></td>\n+ <td><table><tr><td>ucaccgggugaaaaaucaccua</td></tr></table></td>\n+<td><table><tr><td>-</td></tr></table></td>\n+<td>gggucccagagaccuuggugguuuuucucugcagugauagauacuucuaacaacucgcuaucaccgggugaaaaaucaccuaggucuggagccuccu</td>\n+\t\t\t</tr> \n+</table>\n+</body>\n+</html>\n' |
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| diff -r 000000000000 -r 2c039fc73f1f test-data/mature_ref_this_species.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mature_ref_this_species.fa Tue Jan 27 09:06:15 2015 -0500 |
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| @@ -0,0 +1,14 @@ +>cel-miR-36 +TCACCGGGTGAAAATTCGCATG +>cel-miR-37 +TCACCGGGTGAACACTTGCAGT +>cel-miR-38 +TCACCGGGAGAAAAACTGGAGT +>cel-miR-39 +TCACCGGGTGTAAATCAGCTTG +>cel-miR-40 +TCACCGGGTGTACATCAGCTAA +>cel-miR-41 +TCACCGGGTGAAAAATCACCTA +>cel-miR-229 +AATGACACTGGTTATCTTTTCCATCG |
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| diff -r 000000000000 -r 2c039fc73f1f test-data/miRNAs_expressed_all_samples.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/miRNAs_expressed_all_samples.csv Tue Jan 27 09:06:15 2015 -0500 |
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| @@ -0,0 +1,8 @@ +#miRNA read_count precursor total seq seq(norm) +cel-miR-229 4000.00 cel-mir-229 4000.00 4000.00 22896.92 +cel-miR-36 14483.00 cel-mir-36 14483.00 14483.00 82904.02 +cel-miR-37 118131.00 cel-mir-37 118131.00 118131.00 676208.96 +cel-miR-38 2123.00 cel-mir-38 2123.00 2123.00 12152.54 +cel-miR-39 2994.00 cel-mir-39 2994.00 2994.00 17138.34 +cel-miR-40 32878.00 cel-mir-40 32878.00 32878.00 188201.22 +cel-miR-41 87.00 cel-mir-41 87.00 87.00 498.01 |
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| diff -r 000000000000 -r 2c039fc73f1f test-data/precursors_ref_this_species.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/precursors_ref_this_species.fa Tue Jan 27 09:06:15 2015 -0500 |
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| @@ -0,0 +1,14 @@ +>cel-mir-36 +CACCGCTGTCGGGGAACCGCGCCAATTTTCGCTTCAGTGCTAGACCATCCAAAGTGTCTATCACCGGGTGAAAATTCGCATGGGTCCCCGACGCGGA +>cel-mir-37 +TTCTAGAAACCCTTGGACCAGTGTGGGTGTCCGTTGCGGTGCTACATTCTCTAATCTGTATCACCGGGTGAACACTTGCAGTGGTCCTCGTGGTTTCT +>cel-mir-38 +TCTGTGAGCCAGGTCCTGTTCCGGTTTTTTCCGTGGTGATAACGCATCCAAAAGTCTCTATCACCGGGAGAAAAACTGGAGTAGGACCTGTGACTCAT +>cel-mir-39 +TATACCGAGAGCCCAGCTGATTTCGTCTTGGTAATAAGCTCGTCATTGAGATTATCACCGGGTGTAAATCAGCTTGGCTCTGGTGTC +>cel-mir-40 +TCCTGTCCGCACCTCAGTGGATGTATGCCATGATGATAAGATATCAGAAATCCTATCACCGGGTGTACATCAGCTAAGGTGCGGGTACAGGT +>cel-mir-41 +GGGTCCCAGAGACCTTGGTGGTTTTTCTCTGCAGTGATAGATACTTCTAACAACTCGCTATCACCGGGTGAAAAATCACCTAGGTCTGGAGCCTCCT +>cel-mir-229 +CGCCGGCAATGACACTGGTTATCTTTTCCATCGTGGAATGCCCCCCATTGATTTTTTCCCCTTTTCGGGGGGAAAAAATTGGAAACGAGAAAGGTATCGGGTGTCATAGCCGGCG |
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| diff -r 000000000000 -r 2c039fc73f1f test-data/reads_collapsed.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads_collapsed.fa Tue Jan 27 09:06:15 2015 -0500 |
| b |
| b'@@ -0,0 +1,3220 @@\n+>seq_0_x149538\n+TCACCGGGTGGAAACTAGCAGT\n+>seq_149538_x90904\n+TCACCGGGTGAACACTTGCAGT\n+>seq_240442_x25577\n+TCACCGGGTGTACATCAGCTAA\n+>seq_266019_x11571\n+TCACCGGGTGAAAATTCGCATG\n+>seq_277590_x9943\n+TCACCGGGTGGAAACTAGCAG\n+>seq_287533_x5429\n+TCACCGGGTGGAAACTAGCAGTT\n+>seq_292962_x4000\n+AATGACACTGGTTATCTTTTCCATCG\n+>seq_296962_x3796\n+TCACCGGGTGAACACTTGCAG\n+>seq_300758_x2851\n+TCACCGGGTGAACACTTGCAGTT\n+>seq_303609_x2808\n+TCACCGGGGGGAAACTAGCAGT\n+>seq_306417_x2793\n+TCACAGGGTGGAAACTAGCAGT\n+>seq_309210_x2159\n+TCACCGGGTGGAAACTAGCAGTA\n+>seq_311369_x2128\n+TCACCGGGTGTAAATCAGCTTG\n+>seq_313497_x2021\n+TCACCGGGTGGAAACTAGCA\n+>seq_315518_x1866\n+TCACCGGGCGGAAACTAGCAGT\n+>seq_317384_x1629\n+TCACCGGGAGGAAACTAGCAGT\n+>seq_319013_x1597\n+TCACAGGGTGAACACTTGCAGT\n+>seq_320610_x1349\n+TCACCGGGAGAAAAACTGGAGT\n+>seq_321959_x1326\n+TCACCGGGTGGAAAATAGCAGT\n+>seq_323285_x1320\n+TCACCGGGGGAACACTTGCAGT\n+>seq_324605_x1295\n+TCACCGGGTGGANACTAGCAGT\n+>seq_325900_x1251\n+TCACCGGGTGAACACTTGCAGTA\n+>seq_327151_x1237\n+TCACCGGGTGAACACTTGCA\n+>seq_328388_x1017\n+TCACCGGGTGTACATCAGCTA\n+>seq_329405_x990\n+ACCGGGTGGAAACTAGCAGT\n+>seq_330395_x911\n+TCACCGGGTGAANACTTGCAGT\n+>seq_331306_x853\n+TCACCGGGCGAACACTTGCAGT\n+>seq_332159_x841\n+TCACCGGGAGAACACTTGCAGT\n+>seq_333000_x757\n+TCACCGCGTGGAAACTAGCAGT\n+>seq_333757_x746\n+ACCGGGTGAACACTTGCAGT\n+>seq_334503_x690\n+TCACCGGGTGGAAACTAGCAGC\n+>seq_335193_x686\n+TCACCGGGTGAAAACTTGCAGT\n+>seq_335879_x674\n+TCACCGCGTGAACACTTGCAGT\n+>seq_336553_x669\n+TCACCGGGTGGAAACTAGCAGA\n+>seq_337222_x632\n+AGCTGATTTCGTCTTGGTAATA\n+>seq_337854_x604\n+TCAACGGGTGGAAACTAGCAGT\n+>seq_338458_x598\n+TCACCGGGTGGAAACTATCAGT\n+>seq_339056_x557\n+TCACCGGGTGGAAACTAGCAGG\n+>seq_339613_x541\n+TCACCGGGTGTACATCAGCTAAA\n+>seq_340154_x508\n+TCACCGGGTGGACACTAGCAGT\n+>seq_340662_x508\n+TCACCGGGTGAACACTGGCAGT\n+>seq_341170_x448\n+TCACCGGGTGAACACTTTCAGT\n+>seq_341618_x427\n+TCACCGGGTGAACAATTGCAGT\n+>seq_342045_x391\n+TCACCGGGTGAACACTTGCCGT\n+>seq_342436_x389\n+TCACCGGGTGGAAACTTGCAGT\n+>seq_342825_x384\n+TCACAGGGTGTACATCAGCTAA\n+>seq_343209_x360\n+TCACCGGGTGAAAACTAGCAGT\n+>seq_343569_x355\n+TCACCGGGTGTACATCAGCTAAT\n+>seq_343924_x352\n+TCACCGGGTGCAAACTAGCAGT\n+>seq_344276_x345\n+TCACCGGGTGGAGACTAGCAGT\n+>seq_344621_x340\n+TCAACGGGTGAACACTTGCAGT\n+>seq_344961_x338\n+TCACCGGGTGTACATCAGCTAT\n+>seq_345299_x327\n+TCACCGGGTGAACACTTGCTGT\n+>seq_345626_x322\n+TCACCGGGTGGAAATTAGCAGT\n+>seq_345948_x316\n+TCACCGGGTGAAAATTCGCATT\n+>seq_346264_x309\n+TCACCGGGTGGAAACTAGCCGT\n+>seq_346573_x304\n+TCACCGGGTGGTAACTAGCAGT\n+>seq_346877_x304\n+TCACCGGGTGGAAACTAGCTGT\n+>seq_347181_x298\n+TCACAGGGTGAAAATTCGCATG\n+>seq_347479_x287\n+TAACCGGGTGGAAACTAGCAGT\n+>seq_347766_x287\n+TCACCGGGGGTACATCAGCTAA\n+>seq_348053_x285\n+CACCGGGTGAACACTTGCAGT\n+>seq_348338_x283\n+TCACCGGGTGGAAACTAGTAGT\n+>seq_348621_x282\n+TCACCGGGTGGAAACTCGCAGT\n+>seq_348903_x271\n+TCACCGGGTGCACATCAGCTAA\n+>seq_349174_x270\n+TCACCGGGTGAACACTTGCAGC\n+>seq_349444_x269\n+TCACCTGGTGGAAACTAGCAGT\n+>seq_349713_x268\n+TCACCGGGTGTANATCAGCTAA\n+>seq_349981_x265\n+TCACCGGGTTGAAACTAGCAGT\n+>seq_350246_x264\n+TCACCGGGTGGCAACTAGCAGT\n+>seq_350510_x263\n+TCACCGGGTGGAAACTAGAAGT\n+>seq_350773_x263\n+TCACCGGGTGGAAACTACCAGT\n+>seq_351036_x251\n+TCACCGGGGGAAAATTCGCATG\n+>seq_351287_x247\n+TCACCGGGTGGACATCAGCTAA\n+>seq_351534_x242\n+TCACCGGGTGAACACTTGCAGG\n+>seq_351776_x240\n+ACCGGGTGTACATCAGCTAA\n+>seq_352016_x236\n+TCACCGGGTGGAAACTAGNAGT\n+>seq_352252_x230\n+TCACCGGGAGAAAAACTGGAGTT\n+>seq_352482_x229\n+TCACCGGGTGAAAATTCGCAT\n+>seq_352711_x226\n+TCACCGGGTGAAGACTTGCAGT\n+>seq_352937_x224\n+TCACCGGGCGTACATCAGCTAA\n+>seq_353161_x223\n+TCACCGGGTGGAAACTNGCAGT\n+>seq_353384_x221\n+CACCGGGTGAACACTTGCAGTT\n+>seq_353605_x219\n+TCACCGGATGGAAACTAGCAGT\n+>seq_353824_x217\n+TCACCGGGTGGAAACTAGCATT\n+>seq_354041_x214\n+TAACCGGGTGAACACTTGCAGT\n+>seq_354255_x214\n+TCACCGGGTGTAAATCAGCTTT\n+>seq_354469_x212\n+TCACCGGGTTAACACTTGCAGT\n+>seq_354681_x211\n+TCAGCGGGTGGAAACTAGCAGT\n+>seq_354892_x210\n+TCACCGGGTGCACACTTGCAGT\n+>seq_355102_x209\n+TCACCGGCTGGAAACTAGCAGT\n+>seq_355311_x207\n+TCACCGGCTGAACACTTGCAGT\n+>seq_355518_x204\n+TTACCGGGTGGAAACTAGCAGT\n+>seq_355722_x204\n+TCATCGGGTGGAAACTAGCAGT\n+>seq_355926'..b'+AGTGGATGTTTGCCATGATGATA\n+>seq_378232_x1\n+ATCACCGGGGGAACACTTGCAG\n+>seq_378233_x1\n+TCACCGGGTGTAAATTCGCA\n+>seq_378234_x1\n+TCACCGGGTGGAAACTNGCA\n+>seq_378235_x1\n+ACCGGGAGAACACTTGCAG\n+>seq_378236_x1\n+TGTGGGTGTCCGTTGAGGTGCT\n+>seq_378237_x1\n+ACGGGGTGTACATCAGCTAA\n+>seq_378238_x1\n+ACCGGGTGGAGACTAGCAG\n+>seq_378239_x1\n+ACCGGGTGTAAATCTGCTTG\n+>seq_378240_x1\n+TCACCGGGTGTAAATTAGCTT\n+>seq_378241_x1\n+AACACCGGGTGTACATCAGCTAA\n+>seq_378242_x1\n+CTCACCGGGTGTACATCAGCTA\n+>seq_378243_x1\n+TCACCGGGAGAAAAACTGGAT\n+>seq_378244_x1\n+ACCGGGTGAAAATTCGCACG\n+>seq_378245_x1\n+ACCGGGTGAAAATTCGCATC\n+>seq_378246_x1\n+ACCGGGTGGAAGCTAGCAGT\n+>seq_378247_x1\n+ACCGGGAGGAAAACTGGAGT\n+>seq_378248_x1\n+TGTGGGTGTCCGTTGCGGTGTTA\n+>seq_378249_x1\n+AGCTGATTTCGTCTTGGTAATAC\n+>seq_378250_x1\n+TCACCGGGTGTANATCAGCT\n+>seq_378251_x1\n+CCCGGGTGAACACTTGCAGT\n+>seq_378252_x1\n+ACCGGGTGAACACTTGCTGT\n+>seq_378253_x1\n+GCACCGGGTGAACACTTGCA\n+>seq_378254_x1\n+TGTGGGTGTCCGTTGCGGTGC\n+>seq_378255_x1\n+CGCCAATTTTCGCTTCAGCGC\n+>seq_378256_x1\n+TCACCGGGTGGAAACTAGCAGAGGC\n+>seq_378257_x1\n+ACGAAAAGGGGAGCAGAACGA\n+>seq_378258_x1\n+ACTGGGTGAAAATTCGCATG\n+>seq_378259_x1\n+TCACCGGGTGTACATCAGCCA\n+>seq_378260_x1\n+TCACCGGGTTTAAATCAGCTTG\n+>seq_378261_x1\n+TCACCGGGAGAAAATCTGGAGT\n+>seq_378262_x1\n+TAACCGGGTGTAAATCAGCTTG\n+>seq_378263_x1\n+TCACCGGGTGAAAATTCGCATGGC\n+>seq_378264_x1\n+TCACCGGGTGAAGATTCGCAT\n+>seq_378265_x1\n+TAAGCGTCGCGTGTTGTTAAG\n+>seq_378266_x1\n+TCACCGGGTGTACATCAGGTA\n+>seq_378267_x1\n+ACCTGGTGGAAACTAGCAGT\n+>seq_378268_x1\n+TAACCGGGTGAAAATTCGCAT\n+>seq_378269_x1\n+TCACCGGGTGGAAAATAG\n+>seq_378270_x1\n+CCGGGTGTACATCAGCTA\n+>seq_378271_x1\n+ACCGGGTGCACATCAGCTAA\n+>seq_378272_x1\n+TCACCGGGTGTACATGAGCTA\n+>seq_378273_x1\n+TCACCGGGAGTAAAACTGGAG\n+>seq_378274_x1\n+GAAAAGGGGAGCAGAACGAAAAT\n+>seq_378275_x1\n+CACGAAAAGGGGAGCAGAACGA\n+>seq_378276_x1\n+CGAAAAGGGGAGCAGAACGA\n+>seq_378277_x1\n+AGCTGATTTCGTCTTGATAAT\n+>seq_378278_x1\n+ACCGGGTGGAAACTAGCANT\n+>seq_378279_x1\n+ATCACCGGGGGAAAAATCACCTA\n+>seq_378280_x1\n+GGTGGTTTTTCTCTGCAGCGATA\n+>seq_378281_x1\n+TCACCGGGTGAAAAATCATCTA\n+>seq_378282_x1\n+ATCACCGGGTGGAAACTAGCA\n+>seq_378283_x1\n+TCACCGGGTGGAAACTAGCAGTGGTTC\n+>seq_378284_x1\n+CACCGGGTGAACNCTTGCAGT\n+>seq_378285_x1\n+TCACCGGGTGAACACTTGCGG\n+>seq_378286_x1\n+TCACCGGGTGGAAACTAGCAGTGACT\n+>seq_378287_x1\n+CGAAAAGGGGATCTGCAAAAAG\n+>seq_378288_x1\n+CGGGTGGAAACTAGAAGT\n+>seq_378289_x1\n+TTTCTTGTCCAATACATCT\n+>seq_378290_x1\n+TCACCGGGAGAAAAATTGGAG\n+>seq_378291_x1\n+TCACCCGGAGAAAAACTGGAGT\n+>seq_378292_x1\n+CAGCTGATTTCGTCTTGGTAAT\n+>seq_378293_x1\n+CGAAAAGGAGATCTGGCAC\n+>seq_378294_x1\n+TCACCGGGTGAACACTTNCAGT\n+>seq_378295_x1\n+TCANCGGGTGTACATCAGCTA\n+>seq_378296_x1\n+TATCACCGGGTGAAAAATCACCT\n+>seq_378297_x1\n+TAACCGGGTGAAAAATCACCTA\n+>seq_378298_x1\n+TCACCGGGTGGAAACTAGCAGTGGAT\n+>seq_378299_x1\n+TCACCGGGTGAACACTNGCAG\n+>seq_378300_x1\n+AGTGGATGTATGCCATGATGGTA\n+>seq_378301_x1\n+TCACCGGGTGTACGTCAGCTA\n+>seq_378302_x1\n+TAATATCGTCCTTCTTCAT\n+>seq_378303_x1\n+TCACTGGGTGAAAATTCGCAT\n+>seq_378304_x1\n+CGCCAATTTTCGCTTCAGGGCTA\n+>seq_378305_x1\n+AGCTGATTTCGTATTGGTAAT\n+>seq_378306_x1\n+TCAACGGGTGAACACTTG\n+>seq_378307_x1\n+TCACCGGGTGTAAATCAGCTAG\n+>seq_378308_x1\n+TGACCGGGAGAAAAACTGGAGTA\n+>seq_378309_x1\n+GGTATCACCGGGTGAACACTTGCAGT\n+>seq_378310_x1\n+CGCCAATTTTCGCTTCAGTTCT\n+>seq_378311_x1\n+CCACCGGGTGGAAACTAGCAGTGG\n+>seq_378312_x1\n+TCACCGGGTGCAAACTAGCAGTG\n+>seq_378313_x1\n+TCCGGGTGTACATCAGCTAA\n+>seq_378314_x1\n+ATCACCGGGAGTAAAACTGGAGT\n+>seq_378315_x1\n+TGCTGGTTTCTTCCACAGTGG\n+>seq_378316_x1\n+TCACCGGGTGAAAATTAGCA\n+>seq_378317_x1\n+TCAACGGGTGAAAATTCGCAT\n+>seq_378318_x1\n+TNACCGGGTGGAAACTAGCA\n+>seq_378319_x1\n+CAACGGGTGAACACTTGCAG\n+>seq_378320_x1\n+ATCACCGGGTGGAAACTAGCAGG\n+>seq_378321_x1\n+TGTGGGTGTCCGTTGCGGTGATA\n+>seq_378322_x1\n+TCACCGGGTGTAAATCAACT\n+>seq_378323_x1\n+TCACCGGGTGAAAATTCGCAGGG\n+>seq_378324_x1\n+TCACCGGGTGAACACTTGCAGTCG\n+>seq_378325_x1\n+ATCACCGGGTGTACATCACCTA\n+>seq_378326_x1\n+AGTGGATGTATGCTATGATGATA\n+>seq_378327_x1\n+TGATGGTTTCTTCCACAGTGGT\n+>seq_378328_x1\n+AATCACCGGGTGGAAACTAG\n+>seq_378329_x1\n+AGCTGATTACGTCTTGGTAAT\n+>seq_378330_x1\n+ACAGGGTGTACATCAGCTAA\n+>seq_378331_x1\n+TCACCGGGTGTATATCAGCT\n+>seq_378332_x1\n+ACCGGGTGGAAACTAGTAGT\n' |
| b |
| diff -r 000000000000 -r 2c039fc73f1f tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jan 27 09:06:15 2015 -0500 |
| b |
| @@ -0,0 +1,45 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="perl" version="5.18.1"> + <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bowtie" version="0.12.7"> + <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="vienna_rna" version="1.8.5"> + <repository changeset_revision="54e961ee33d4" name="package_vienna_rna_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="pdf_api2" version="2.023"> + <repository changeset_revision="b9b7fadfdb69" name="package_perl_pdf_api2_2_023" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="mirdeep2_quantifier" version="2.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-quantifier.tar.gz</action> + <action type="move_file"> + <source>quantifier.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>make_html2.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>convert_bowtie_output.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + +The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. +First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. +By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. +The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined. + + </readme> + </package> +</tool_dependency> |