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Commit message:
Uploaded v3.0.1b (still working on this prior to main Tool Shed release) |
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modified:
gmap.xml gmap_build.xml gsnap.xml iit_store.xml lib/galaxy/datatypes/gmap.py snpindex.xml tool_dependencies.xml |
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added:
README.rst gmap_v3.0.1b.tar.gz test-data/gmap_indices.loc test-data/ss.chr17.fasta test-data/ss.her2.chr17.txt test-data/ss.her2.fasta tool-data/tool_data_table_conf.xml.sample |
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README |
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| diff -r a88571642c6e -r 14561eb803a5 README --- a/README Wed Sep 28 10:49:02 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,71 +0,0 @@ -GMAP applications and citation info are available from: http://research-pub.gene.com/gmap/ - - - Installation instructions are in the README file in the download, - and online: http://research-pub.gene.com/gmap/src/README - - These tools were consistent with gmap version: 2011-11-30 - - -GMAP and GSNAP use added datatypes: - - add datatype definition file: lib/galaxy/datatypes/gmap.py - - add the following import line to: lib/galaxy/datatypes/registry.py - import gmap # added for gmap tools - - add to datatypes_conf.xml - <!-- Start GMAP Datatypes --> - <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/> - <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/> - <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/> - <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" display_in_upload="True"/> - <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/> - <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/> - <datatype extension="tally.iit" type="galaxy.datatypes.gmap:TallyIntervalIndexTree" display_in_upload="True"/> - <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/> - <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/> - <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/> - <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/> - <datatype extension="gsnap_tally" type="galaxy.datatypes.gmap:TallyAnnotation" display_in_upload="True"/> - <datatype extension="gsnap" type="galaxy.datatypes.gmap:GsnapResult" display_in_upload="True"/> - <!-- End GMAP Datatypes --> - -Tools: - GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations - GMAP - map sequences to a reference sequence GmapDB index - GSNAP - align sequences to a reference and detect splicing - - Add to tool_conf.xml ( probably in the "NGS: Mapping" section ) - <tool file="gmap/gmap.xml" /> - <tool file="gmap/gsnap.xml" /> - <tool file="gmap/gmap_build.xml" /> - <tool file="gmap/snpindex.xml" /> - <tool file="gmap/iit_store.xml" /> - -Admin built cached gmapdb indexes defined in tool-data/gmap_indices.loc - - -TODO: - - - Add classes to gmap.py - CmetIndex - an index created by cmetindex - AtoiIndex - an index created by atoiindex - - Add tally creation - gsnap default output -> gsnap_tally -> iit_store - - Add goby support - Should add separate tools and datatypes for goby - GSNAP goby output relies on goby input, might be better to have a separate gsnap tool for goby - - Possibly add Tools: - get_genome - retrieves from a gmapdb - cmetindex - create methylcytosine index - atoiindex - create A-to-I RNA editing index - - - - - |
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| diff -r a88571642c6e -r 14561eb803a5 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Oct 21 10:55:40 2016 -0400 |
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| @@ -0,0 +1,108 @@ +Galaxy Wrapper for GMAP +======================= + +This wrapper is copyright 2011, 2013 by Jim Johnson (Minnesota Supercomputing +Institute, University of Minnesota). +Revisions copyright 2016 by Peter Cock (The James Hutton Institute, UK). + +This Galaxy wrapper is available from the Galaxy Tool Shed at: + +toolshed.g2.bx.psu.edu/view/jjohnson/gmap + +GMAP applications and citation info are available from: +ttp://research-pub.gene.com/gmap/ + +Manual GMAP installation instructions are in the README file in the download, +and online: http://research-pub.gene.com/gmap/src/README + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v2.0.0 - Initial release, for GMAP version 2011-10-07 (by JJ, October 2011). +v2.0.1 - Updated for GMAP version 2011-11-30 (by JJ, November 2011). +v3.0.0 - Work in progress for GMAP version 2013-05-09 (by JJ, June 2013), + never released to the main Galaxy Tool Shed. +v3.0.1 - Various style updates (Peter Cock, October 2016). +======= ====================================================================== + + +Automated Installation +====================== + +This should be straightforward using the Galaxy Tool Shed, which should be +able to automatically install GMAP as well. + + + +Manual Installation +=================== + +GMAP and GSNAP use added datatypes: + +- add datatype definition file: ``lib/galaxy/datatypes/gmap.py`` + +- add the following import line to: ``lib/galaxy/datatypes/registry.py``:: + + import gmap # added for gmap tools + +- add to ``datatypes_conf.xml``:: + + <!-- Start GMAP Datatypes --> + <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/> + <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/> + <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/> + <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" display_in_upload="True"/> + <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/> + <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/> + <datatype extension="tally.iit" type="galaxy.datatypes.gmap:TallyIntervalIndexTree" display_in_upload="True"/> + <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/> + <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/> + <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/> + <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/> + <datatype extension="gsnap_tally" type="galaxy.datatypes.gmap:TallyAnnotation" display_in_upload="True"/> + <datatype extension="gsnap" type="galaxy.datatypes.gmap:GsnapResult" display_in_upload="True"/> + <!-- End GMAP Datatypes --> + +Tools: + +- GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations +- GMAP - map sequences to a reference sequence GmapDB index +- GSNAP - align sequences to a reference and detect splicing + +Add to ``tool_conf.xml`` (probably in the "NGS: Mapping" section):: + + <tool file="gmap/gmap.xml" /> + <tool file="gmap/gsnap.xml" /> + <tool file="gmap/gmap_build.xml" /> + <tool file="gmap/snpindex.xml" /> + <tool file="gmap/iit_store.xml" /> + +Admin built cached gmapdb indexes defined in ``tool-data/gmap_indices.loc`` + + +TODO +==== + +- Add classes to ``gmap.py`` + + - CmetIndex - an index created by cmetindex + - AtoiIndex - an index created by atoiindex + +- Add tally creation + + - gsnap default output -> gsnap_tally -> iit_store + +- Add goby support + + - Should add separate tools and datatypes for goby + - GSNAP goby output relies on goby input, might be better to have a separate gsnap tool for goby + +- Possibly add Tools: + + - get_genome - retrieves from a gmapdb + - cmetindex - create methylcytosine index + - atoiindex - create A-to-I RNA editing index |
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| diff -r a88571642c6e -r 14561eb803a5 gmap.xml --- a/gmap.xml Wed Sep 28 10:49:02 2016 -0400 +++ b/gmap.xml Fri Oct 21 10:55:40 2016 -0400 |
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| b'@@ -4,19 +4,19 @@\n <requirement type="package" version="2013-05-09">gmap</requirement>\n </requirements>\n <version_command>gmap --version</version_command>\n- <command>\n+ <command detect_errors="exit_code"><![CDATA[\n #import os,os.path\n gmap\n- --nthreads=4 --ordered\n+ --nthreads=\\${GALAXY_SLOTS:-4} --ordered\n #if $refGenomeSource.genomeSource == "history":\n --gseg=$refGenomeSource.ownFile\n #elif $refGenomeSource.genomeSource == "gmapdb":\n- --dir=$refGenomeSource.gmapdb.extra_files_path --db=$refGenomeSource.gmapdb.metadata.db_name\n+ --dir=\'$refGenomeSource.gmapdb.extra_files_path\' --db=\'$refGenomeSource.gmapdb.metadata.db_name\'\n #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2:\n --kmer=$refGenomeSource.kmer\n #end if\n #else:\n- --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value)\n+ --dir=\'$os.path.dirname($refGenomeSource.gmapindex.value)\' --db=\'$os.path.basename($refGenomeSource.gmapindex.value)\'\n #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2:\n --kmer=$refGenomeSource.kmer\n #end if\n@@ -45,11 +45,6 @@\n $result.sam_use_0M\n $result.force_xs_dir\n $result.md_lowercase_snp\n- #* Removed in gmap version 2011-11-30\n- #if len($result.noncanonical_splices.__str__) > 0\n- --noncanonical-splices=$result.noncanonical_splices\n- #end if\n- *#\n #if len($result.read_group_id.__str__) > 0\n --read-group-id=$result.read_group_id\n #end if\n@@ -116,9 +111,7 @@\n --wraplength=$advanced.wraplength\n #end if\n #end if\n- #if $split_output == True\n- $split_output\n- #end if\n+ $split_output\n #if len($quality_protocol.__str__) > 0:\n --quality-protocol=$quality_protocol\n #end if\n@@ -126,15 +119,15 @@\n #for $i in $inputs:\n ${i.added_input}\n #end for\n- #if $split_output == True\n+ #if $split_output\n 2> $gmap_stderr\n #else\n 2> $gmap_stderr > $output\n #end if\n- </command>\n+ ]]></command>\n <inputs>\n <!-- Input data -->\n- <param name="input" type="data" format="fasta,fastqsanger,fastqillumina" label="<H2>Input Sequences</H2>Select an mRNA or EST dataset to map" />\n+ <param name="input" type="data" format="fasta,fastqsanger,fastqillumina" label="Input Sequences" help="Select an mRNA or EST dataset to map" />\n <repeat name="inputs" title="addtional mRNA or EST dataset to map">\n <param name="added_input" type="data" format="fasta,fastqsanger,fastqillumina" label=""/>\n </repeat>\n@@ -146,14 +139,14 @@\n \n <!-- GMAPDB for mapping -->\n <conditional name="refGenomeSource">\n- <param name="genomeSource" type="select" label="<HR><H2>Map To</H2>Will you map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">\n+ <param name="genomeSource" type="select" label="Map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">\n <option value="indexed">Use a built-in index</option>\n <option value="gmapdb">Use gmapdb from the history</option>\n <option value="history">Use a fasta reference sequence from the history</option>\n </param>\n <when value="indexed">\n <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">\n- <options from_file="gmap_indices.loc">\n+ <options from_data_table="gmap_indices">\n <column name="uid" index="0" />\n <column name="dbkey" index="1" />\n <column name="name" index="2" />\n@@ -164,7 +157,7 @@\n </options>\n </param>\n <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults'..b' flags to indicate whether the read is the first or second end of a pair"/>\n+ <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print SAM headers (lines beginning with \'@\')"/>\n <param name="read_group_id" type="text" value="" label="Value to put into read-group id (RG-ID) field"/>\n <param name="read_group_name" type="text" value="" label="Value to put into read-group name (RG-SM) field"/>\n <param name="read_group_library" type="text" value="" label="Value to put into read-group library (RG-LB) field"/>\n@@ -484,18 +470,50 @@\n </data>\n </outputs>\n <tests>\n+ <test>\n+ <!-- \n+ mimic first test from GMAP source code, mapping Human ERBB2 onto fragment of chr17\n+ $ gmap -A -g ss.chr17test ss.her2\n+ -->\n+ <param name="input" value="ss.her2.fasta" ftype="fasta"/>\n+ <!-- <param name="quality_protocol" value=""/> -->\n+ <param name="genomeSource" value="history"/>\n+ <param name="ownFile" value="ss.chr17.fasta" ftype="fasta"/>\n+ <param name="format" value="align"/>\n+ <param name="computation" value="default"/>\n+ <param name="options" value="default"/>\n+ <output name="output" file="ss.her2.chr17.txt" ftype="txt"/>\n+ </test>\n </tests>\n \n <help>\n \n **What it does**\n \n-GMAP_ (Genomic Mapping and Alignment Program) The functionality provided by gmap allows a user to: (1) map and align a single cDNA interactively against a large genome in about a second, without the startup time of several minutes typically needed by existing mapping programs; (2) switch arbitrarily among different genomes, without the need for a preloaded server dedicated to each genome; (3) run the program on computers with as little as 128 MB of RAM (random access memory); (4) perform high-throughput batch processing of cDNAs by using memory mapping and multithreading when appropriate memory and hardware are available; (5) generate accurate gene models, even in the presence of substantial polymorphisms and sequence errors; (6) locate splice sites accurately without the use of probabilistic splice site models, allowing generalized use of the program across species; (7) detect statistically significant microexons and incorporate them into the alignment; and (8) handle mapping and alignment tasks on genomes having alternate assemblies, linkage groups or strains. It is developed by Thomas D. Wu of Genentech, Inc.\n+GMAP (Genomic Mapping and Alignment Program)\n+\n+The functionality provided by gmap allows a user to:\n \n-Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310\n+ 1. map and align a single cDNA interactively against a large genome in\n+ about a second, without the startup time of several minutes typically\n+ needed by existing mapping programs;\n+ 2. switch arbitrarily among different genomes, without the need for a\n+ preloaded server dedicated to each genome;\n+ 3. run the program on computers with as little as 128 MB of RAM (random\n+ access memory)\n+ 4. perform high-throughput batch processing of cDNAs by using memory\n+ mapping and multithreading when appropriate memory and hardware are\n+ available;\n+ 5. generate accurate gene models, even in the presence of substantial\n+ polymorphisms and sequence errors;\n+ 6. locate splice sites accurately without the use of probabilistic splice\n+ site models, allowing generalized use of the program across species;\n+ 7. detect statistically significant microexons and incorporate them into\n+ the alignment; and\n+ 8. handle mapping and alignment tasks on genomes having alternate\n+ assemblies, linkage groups or strains.\n \n-.. _GMAP: http://research-pub.gene.com/gmap/\n-.. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859\n+It is developed by Thomas D. Wu of Genentech, Inc.\n \n ------\n \n' |
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| diff -r a88571642c6e -r 14561eb803a5 gmap_build.xml --- a/gmap_build.xml Wed Sep 28 10:49:02 2016 -0400 +++ b/gmap_build.xml Fri Oct 21 10:55:40 2016 -0400 |
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| @@ -4,7 +4,9 @@ <requirement type="package" version="2013-05-09">gmap</requirement> </requirements> <version_command>gmap --version</version_command> - <command interpreter="command"> /bin/bash $shscript > $output </command> + <command detect_errors="exit_code"><![CDATA[ +/bin/bash $shscript > $output + ]]></command> <configfiles> <configfile name="shscript"> #!/bin/bash @@ -183,9 +185,6 @@ <option value="15" selected="true">15 (4GB RAM)</option> </param> </inputs> - <stdio> - <exit_code range="1" level="fatal" description="Error running gmap_build" /> - </stdio> <outputs> <!-- <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/> |
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| diff -r a88571642c6e -r 14561eb803a5 gmap_v3.0.1b.tar.gz |
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| Binary file gmap_v3.0.1b.tar.gz has changed |
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| diff -r a88571642c6e -r 14561eb803a5 gsnap.xml --- a/gsnap.xml Wed Sep 28 10:49:02 2016 -0400 +++ b/gsnap.xml Fri Oct 21 10:55:40 2016 -0400 |
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| @@ -4,7 +4,7 @@ <requirement type="package" version="2013-05-09">gmap</requirement> </requirements> <version_command>gsnap --version</version_command> - <command> + <command detect_errors="exit_code"><![CDATA[ #import os.path, re gsnap --nthreads="4" --ordered @@ -234,8 +234,7 @@ 2> $gsnap_stderr > $gsnap_out #end if #end if - - </command> + ]]></command> <inputs> <!-- Input data --> <conditional name="seq"> @@ -319,7 +318,7 @@ </param> <when value="indexed"> <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="gmap_indices.loc"> + <options from_data_table="gmap_indices"> <column name="uid" index="0" /> <column name="dbkey" index="1" /> <column name="name" index="2" /> @@ -331,7 +330,7 @@ </param> <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size"> - <options from_file="gmap_indices.loc"> + <options from_data_table="gmap_indices"> <column name="name" index="3"/> <column name="value" index="3"/> <filter type="param_value" ref="gmapindex" column="6"/> @@ -364,7 +363,7 @@ </when> <when value="gmapdb"> <param name="splicemap" type="select" data_ref="gmapindex" label="Use map for splicing involving known sites or known introns" help=""> - <options from_file="gmap_indices.loc"> + <options from_data_table="gmap_indices"> <column name="name" index="4"/> <column name="value" index="4"/> <filter type="param_value" ref="gmapindex" column="6"/> @@ -389,7 +388,7 @@ </when> <when value="gmapdb"> <param name="snpindex" type="select" data_ref="gmapindex" label="Use database containing known SNPs" help=""> - <options from_file="gmap_indices.loc"> + <options from_data_table="gmap_indices"> <column name="name" index="5"/> <column name="value" index="5"/> <filter type="param_value" ref="gmapindex" column="6"/> @@ -810,7 +809,7 @@ <tests> </tests> - <help> + <help><![CDATA[ **What it does** @@ -844,12 +843,12 @@ paired-end read). The same FASTA file can have a mixture of single-end and paired-end reads of varying lengths, if desired. -Single-end reads: +*Single-end reads*: -Each FASTA entry should contain one short read per line, like this +Each FASTA entry should contain one short read per line, like this:: ->Header information -AAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTA + >Header information + AAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTA Each short read can have a different length. However, the entire read needs to be on a single line, and may not wrap around multiple lines. @@ -857,14 +856,14 @@ paired-end. -Paired-end reads: +*Paired-end reads*: Each FASTA entry should contain two short reads, one per line, like -this +this:: ->Header information -AAAACATTCTCCTCCGCATAAGCCTAGTAGATTA -GGCGTAGGTAGAAGTAGAGGTTAAGGCGCGTCAG + >Header information + AAAACATTCTCCTCCGCATAAGCCTAGTAGATTA + GGCGTAGGTAGAAGTAGAGGTTAAGGCGCGTCAG By default, the program assumes that the second end is in the reverse complement direction compared with the first end. If they are in the @@ -879,8 +878,10 @@ SAM output format Default GSNAP format - See the README_ - </help> + +See the README_ + + ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btq057</citation> </citations> |
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| diff -r a88571642c6e -r 14561eb803a5 iit_store.xml --- a/iit_store.xml Wed Sep 28 10:49:02 2016 -0400 +++ b/iit_store.xml Fri Oct 21 10:55:40 2016 -0400 |
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| @@ -4,7 +4,9 @@ <requirement type="package" version="2013-05-09">gmap</requirement> </requirements> <version_command>iit_store --version</version_command> - <command interpreter="command"> /bin/bash $shscript 2> $log </command> + <command detect_errors="exit_code" interpreter="bash"><![CDATA[ +$shscript 2> $log + ]]></command> <configfiles> <configfile name="shscript"> #!/bin/bash |
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| diff -r a88571642c6e -r 14561eb803a5 lib/galaxy/datatypes/gmap.py --- a/lib/galaxy/datatypes/gmap.py Wed Sep 28 10:49:02 2016 -0400 +++ b/lib/galaxy/datatypes/gmap.py Fri Oct 21 10:55:40 2016 -0400 |
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| @@ -471,7 +471,7 @@ pat = '>(\S+\.intron\d+)\s((\S+):(\d+)\.\.(\d+))\s(donor|acceptor)(\s(\d+))?$' fh = open(filename) count = 0 - while True and count < 10: + while count < 10: line = fh.readline() if not line: break # EOF |
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| diff -r a88571642c6e -r 14561eb803a5 snpindex.xml --- a/snpindex.xml Wed Sep 28 10:49:02 2016 -0400 +++ b/snpindex.xml Fri Oct 21 10:55:40 2016 -0400 |
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| @@ -4,9 +4,11 @@ <requirement type="package" version="2013-05-09">gmap</requirement> </requirements> <version_command>snpindex --version</version_command> - <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command> + <command detect_errors="exit_code" interpreter="bash"><![CDATA[ +$shscript 2>1 1> $output + ]]></command> <configfiles> - <configfile name="shscript"> + <configfile name="shscript"><![CDATA[ #!/bin/bash #set $ds = chr(36) #set $gt = chr(62) @@ -41,7 +43,7 @@ snpindex -D $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit echo snpindex -D $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit #end if - </configfile> + ]]></configfile> </configfiles> <inputs> <conditional name="refGenomeSource"> @@ -51,7 +53,7 @@ </param> <when value="indexed"> <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="gmap_indices.loc"> + <options from_data_table="gmap_indices"> <column name="uid" index="0" /> <column name="dbkey" index="1" /> <column name="name" index="2" /> |
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| diff -r a88571642c6e -r 14561eb803a5 test-data/gmap_indices.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gmap_indices.loc Fri Oct 21 10:55:40 2016 -0400 |
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| @@ -0,0 +1,5 @@ +# This will contain any test genome index files +# +# Having a file present, even empty, is currently +# apparently needed to avoid a Galaxy bug - see +# https://github.com/galaxyproject/galaxy/issues/2987 \ No newline at end of file |
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| diff -r a88571642c6e -r 14561eb803a5 test-data/ss.chr17.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ss.chr17.fasta Fri Oct 21 10:55:40 2016 -0400 |
| b |
| b'@@ -0,0 +1,3335 @@\n+>chr17test\n+CATGTGTTTTGCAGGGACATGGGTGAAGCTAGAAGCCATTATTCTCCACAAACTAATGCA\n+GGAACAGAAAACCAAACACTGCATGCTCTCACTTGTAAGTGGGAGCTGAATGCTGGGATC\n+ACATGGACACGGGGAGGGGAACAACACACACTAAGGCCTGTCAGAGGGTGGGGTGGGGGA\n+GGGAGAGTATTAGGAAGGATGACTAATGCATTCTGGGCTTAATATCTAGGTGATGGGTTG\n+ATAGGTGCAGTAAACCACTATGGCACACGTTTACCTATGTAACAAACCTGCACATCCTGC\n+ACAGGTACCCCAGAACTAAAAACAATAAAGGGTTCATGTGAGGCTTCCCTGGCCCTGAGG\n+GATGGAGGCCTGGATGCCCACACCAAGGGAGTCTCCTCTCACCACCACACTCTATTGCTT\n+CCTGGCTTGTCCTTTAGCGTTTTTTTGTTGTTGTTGTTTTGTTGTTGTTTTGTTTTTAAT\n+TTGAGACAGGGTCTCGCTCTATCGCCCAGGCTGGAGTGCAGTGATGCGATCTCGGCACAC\n+TGCAGTCTCCACCTCCCAGGTTCAAGTGATTCTCATGTCTCAGCCTCCCAGGTAGATGGG\n+ATTATAGGCGTGCACCACCACGCCCAGCTAATTTTTGTATTTTTAGTGGAGACAGGGTTT\n+CACCACGTTGGCCAGGTTGGTCTCGAACTCCTGACCTCAGATGATCCGCCTGCCTCGGCC\n+TCCCAAAGTGCTGACATTATAGGCTCGAGCCACCATGCCCGGCCTGTCCTTTAGCTTTTT\n+TACATGTCTAACTTCCATTCTTCCTGCTATTCTTGGAAATGCATCTCTCTAGTTTGGAGA\n+GGGAATTTTGGAGAGAGAATTCTGTCATTCTCAGTTCCCTTTAACTGTCTAAGTTCCTGA\n+AATTCTACCACAAAATTCATACTATACTCGTATTCATTGAGTACCCACTATGGGTCAGAT\n+ACTATGCTAGAAGCGTTGGCTACATTATTTCGTTAAATCTTGCTGACCACTCTTTCCACA\n+GTATTAATAATACAATAATAATAACAGTAGTAATAAAACAATAATAGTGACCACTTAATG\n+AAAACTCACTTGAACTAAGTGCTTTACATTAATTGTCATTTTAAAATCTCATTGGGAAAT\n+AACCTACCCAGGGTCAAATAGCCAGTTAGGAATGGGATGAGAAACCTGGACTTCTCTCCA\n+GTACACCAGACTCTCTTGGGGGATGAGGACTTTGGCTGCATGGGTGGAGGAAGGGCAGAG\n+GCATTGTGATGCCTTTCTCTTCCTTCTCATTTATTCTTTCAAATGGAGCACAGAGGCAGC\n+AATATCTTTCCAGACTTCCTTGGGTGCAGAGGGCAGGCACCCCTGATGACAACTCCAGGG\n+CCTGCCCTTTGCTGGGGAAATGTGACCATTTCTTGGGGAGGGCACAGCTCTCACAAGACT\n+TACCAGACCCTTAGAGCAGTTGCCTGGTGTCATAGGAGGTAGGTTCCCATCTGTGTAGTG\n+CAGGATCCTGCTCTGTGATACAAAAGGCTGATTCTTGTATTCATCCTCTGAGGATGGCTT\n+TGGTGTTTGTGCAGGTGCATTTACCCTTCTGTATATGTGTGTGTGCATTTGTGTAATAAT\n+TGGTGTGCAAAGGACCAGGTGATTTGCACACATGCATGCAAGTCAGAACAGCCTGGATTC\n+TGTGCATTTCTCTCAGGATATGTGTGTGTGAAGGGATGATTATCTGGTTGTCTGGGGCCT\n+CAGAAAGGCAGGTAACTTGTAAATTTCCTCAAGCATGTGCTGGTGGGTGGAGTTCCCACA\n+GGATGGAAAAAGGGGCTGGCCCCAGAGTTGAGTTCTGAGCTCAGCTCTCCACCTCTTCCT\n+GCCCGTCTCCAGCTCGCTGCCTCCCCCTACTTTTCCCCAAGCTGGGCAGAATGCCCTCAG\n+CCTGTGCCGGCTGGCACACATGCCACATGGTGCCTGGCGCGCGTCTGGGCAAGGATGACG\n+CCCCCAGGACCGGCTGGGATACCAAGCCACCCGCTGCCTCCCCCACCTCCAGAACGGAGC\n+GTCCCCATCCCATCCCCTTTCCCAGCCAGGGACTCGGGGAGCAGGCAGGGACACAGCACA\n+GACAGATACAAACACACAGATGCACCCAGAGACGCCCACAGGCGTGTGCCCCAGAGGGAC\n+ACAGACACAGGCGTTCACACAGGCTCGGGTACACACACGCACGCTCACACCCCCCCAGAG\n+AAATTTATGAGTGGTCACCACTTGCACGGATCCAGACAGAACCTGACCCGCCTAGGACAT\n+TTAGGCAAATCCACCTGGTGTCTCTGTCCGTGGTGCTGAAACAAGAATGTTTGAACGTCC\n+TCCCTATGGAAGCACTAACAGGAAGTAGAAGGGAGAAAAAGACCTGGGAATGGGTGGTGG\n+ACAAAAAAGAAGCAATGGAGGAGAAAGAAGAGAGGGGAGAGAGAAATCTGGTGGTAAGGG\n+AGATAGAATGTAAAGGATTCCAGGAGGACCAAGGACTGTCTGAACCCTGGGACTAGGAGA\n+GGAAGAAGAGGATGGAAGATGATCTCAGCCCCATCCCTGTCCCCTGAATGTGTGGCTCCT\n+GTGGCCTCCAGTTACTCCTTCCATATGCCACCTTGCCCTAGATGACCTGAAAATAGTAGG\n+GAAAGGAGATGGACCTGGGAAAGCCCTATAGTGGACCTGCAGATAGCTCCCTACCTGATT\n+ACTTATCTCAATTTGTGTTGGGCAAGTGGACAACACTGTTGATCTGGATTTGTTCTGGGG\n+ATTGCAGGGATTTAGTGACTGCTTAATGCTTATCCATCAGATTGGATTATGGGTTCCTTT\n+TGCTGTCTCCTGAGGAAAAAACAACAACAACAACAACAACAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAACTTCCCTTCAGAGAGATTGCATCCCTAATAGGGATGGCTCTCCCATCAGCA\n+GCCCCTTAGTTGTGGAATTTATGTAACATGAGGAATGCCCACTCTTCTGGTGGGGAGACA\n+TCTTCAAGGACTGAAGGGGTTATCATATAACTAGGTGGAAGGGGATAAGGGAAGACGGGA\n+GAGAGAAAAAAGAGAAAAGAGAAGGAGAAAGAATGTGTGTGATGGATGAGAGGATGAAAG\n+AAGGAAGGAAAGAGGGAGGAAGAGGGTGGAGATGCAGATGGCAAGAGTAAGGCAGGGCTT\n+GAGTGAACCAGACAGACTCCTGTGTCCAGGGAAGGGGCAGGGAAAGTGTGCCAGTTGGAG\n+CAAATTGCTCCCCTCAAGTGTCCCAGGGGCCCAGATAAGACTGGAATTCCAGCCTAGTCC\n+TGCAGCTGTTCACAGTGGCATTCTTCACCCAGAGCTTTGGGCAAAAAGACCCTGTGGGCC\n+AGGACTACCGATGTGAGGAGCAGCTGCTCTGGCGAGGAAGGTGAGGTCAGATGCAGTCAA\n+GTGCATGTGTGGTTTCCTCATGGGTGGGGTGAGGACAGTGGGTGTCTCCTGGGGTGTTTC\n+CACCTATTCATATGTAAGCAGTGGCAGGAGGCAGATGCCACATGCTTGGGTAGGCCCTGG\n+AGAGTGGGTACTGGGTTAATTGAGGATGAGGAGCAGGCAGAGGAAAAGGAAGAAGAGAGC\n+AGAGGGAGAGGAGTAAGTAGGAAGAAAAGGATATTGGATCGTCTTCTAGAAAGTTCTGGA\n+CCTTCTGTTATTCTCTTTTCTTCCTACAATTTGAGAAAAAGGCCTAGGCTCAGCTGGGTA\n+TGGTGGCTCATGCCTGTAATCCTAGCACTTTGGGAGGCTGAGGCGGGTGGATCACTTGAC\n+TCTAGGAGTTTGAGACCAGCCTGGGCAACATGGCGAGACTCCATTTCTACAAAAATATAA\n'..b'CTCTCTTT\n+CATTCTAGCTTTAAATATTAGTGATTCTACTTGGAATATGATAGATTTCATAGCTTGGGA\n+ATCTCTTACAGTGAGAGCTTTGCCTATTGTCTGAAATACAGAACTGCAAGTAGAGATGCC\n+TACATTCCGTCCTTGAGCGAGTACTGCCTGACTGCCATGAAGCATGCCACTTAAGATGTC\n+AAAATCTTTCCTAGCAAGCAGACTCAGATAAAAGCAAAACAAAGAGAAGATGTCAAAACC\n+CAAATATTAGGTTTTTCTTTTTATTTTATTATTATTGTTTTAGAGATGGTGTCTTGCTTT\n+GTTGCCCAGGTTGGGCTTGAGCTCCTGGGCTCAAGCAATCCTCTTGCCTCAGCCTCCTCA\n+GCAGCTAGGACTACAGGTGTGTACCACTGTGTATGACCTGTTTGTTTTTTATAAGGGGGT\n+AAACATTTCTTTTTATTTGGATAAGCTTTATCCAAATAAGTTGGATTTCCTTTATCAAAT\n+TAGAAATCCAACTCCTTGATAAAACCAAAGATGCCATTAGGATAAAAAGCAGAAGCACTG\n+CAAGCCATCAGAATTCAGTTGGCCAGCTCCTAACATCATGCAATAGGTTTTATCTAAAAT\n+AAAAGTTTCCTCTCACTCAAAATGAGGGCAGTTTAGGTAGTCATTTCTACTCCATTTTTC\n+CTGAGTTTCACATTATTTCTGTCATCTTTTTGTAACTTTTCTGTTTTAGCCTATTCAAAC\n+TACTCAACTGCAACAATTGCTGTCAAACACTAAATCCCATGAGGGTTTGTACCTATTCTA\n+AATAAGCAATTGGTTCAAGTTACCAAATAAAAATGTCAGACAACCCAAGCTGCAGAACCA\n+GGCTGACAGCCAACTCAATGGGACAAAGGACAGCTGAAGAGATGTGACACAAAAAAGTTT\n+CAGGCTGTTCCAACAAAGAATTAAAAGGAAATAAAACCACAATTGAGATATAGAAGAACA\n+TCTAGTGTTTCAACCAATTGCCAGTAGGCATCTAATTCAAATCACTGAATAAAACAAGGA\n+ATCCCCAAAGCCAAATAGAAGCATCACAATAAATCATATGAGTAGACAAGGATATAAATT\n+GGGCCCTGTGCAAAGAAAATCCTTGTAGTTTTAATTGCCTCTTCCCTAGCCACTCCCCAA\n+CCTCCTCTACCCTCAATTTTTGCCATTTTTTGTAAACGACAACTCCACTCTTCATCAATC\n+TGTTAGGAAATCTTGTTGACTCTACCTTTAAATATACAGAGAATTAGAATACTTCTCACC\n+ACCTCTACCACTAACAAGACATAATTTTCTCTTGCTTGAATTATTGCAATGGCCTCCTAA\n+CTGGACCCCCAATTTCCAACCTTGCCCCAAATACAATCTCTTCTCAAAAGCAAGTAGAGT\n+GATTCTTTCAAATGAGAAGACCAATGATGTCACCTCTTTGTACAAAACCCTCTAAAGATT\n+TTTAATTTCACTCAGAGTAAAAGCCAAAGCCTTTACAATGGCCTGCAAGGCCTGAGAAGA\n+TCTGGTTTCCCATTTCCTCTCTGGCTTCAGGTCCCATTACTCACTGTGTTCCAGACACAC\n+AGAACTACGTACACTTCTTCAAATTTGTGCCCCAGGGCCTTTGCTCTTGCTGTTCCCTAG\n+TTATCTGCAGGGCTTACTCACCCTGTTAAGAAGTCTGTTAAAATGTTACCTCGTTGAAGC\n+CTTCCCTGATTCTCACCCTCACTCCTCAGCAACTGCTTCATTTTTCTCAATAGCACTTAC\n+CACCCGCTAACCTTCCAACTTACAGTTTGCTCATTTACTTTCTTTATAATCTGTCTGCCC\n+CCAGTAAAATATAAACTCCACGAGTCTTTTTACTTACTATTGTATCTCACCACCTAGGAC\n+AGCAGATGCTCACTAAACGTGTGTTGCGTGAACTCACCAGTGTCCCCTGGGTCAGTGCTC\n+TGAAGAAATGTACGGCAGCGCTCCTTGTGCTCCTCAAGGGAACTTCTCTGCTTGTAACTC\n+CTTCCACAAAACTCACATTTGTAGGGTTTCTCCACTAGAAGGAGAACATAAGGGGCACTC\n+AGTGACCCTCAGGGGTTCCACACAGGTCAGGTATTGGGGCTCTGTGACAACTGTTCACTA\n+GAAATGAGACTGCTGAGTGAAGCCAGAGTATTTGGATACTTTTGAATCTATATTTTAAAT\n+TTGGTAAGCTTAAATAAGGTTATGGTCTATGATTAATTATTACGTCAGAGTATTCTTCAA\n+AAGGATCGCCTCCTATCACAAATGGAAGAATTTGGATTTAGTGATTACCATTTCGCATAC\n+TGTTTTGGCTCCAGGTCAAATTTTGTTTTCTTTGGGAAAAAGAAAATAGGGCCCTTTTAT\n+TCTTCAAGGAGGTTAATGTGGTATAAGCAATGAAATAGGAAAGGATTCTTTATTTTGGAC\n+ATCCATCTGGCTGTAAGTAAAGATTGCTGTAGTTTGTGGGAGTTAGCCATTCGGCTAGAA\n+ACTGATGGCCTTTTCAGAACATTGACATATTTGGGTAAATTTAGCTCATCCTTGCCACGT\n+GGCTATAGCAAAGTCTAGGCTAAAACAATAAAAACTGAGCTAATTAACTACGGATTTTTT\n+TGTTTTTTTGTTTTTGAGACAGGGTCTCACTCTATCACCCAGGCTTGGGTGCAGTGGTGA\n+AATCACAGCTCGCTACAGCCCCAATTTCATAGGCTCAGGTGAAGTCTGGGCCTCCCAAAG\n+GCCACCTTGGCCTCCCAAAGTGAGAGGCTTACAGGTGTGAGCCATTGCACCCGGCCAGGA\n+TATTTTTGAATAATAGAAATAAAAATAGGCCGGGCGCAGTGGCTGACACCTGTAATCCCA\n+GCACTTTGGGAGGCCGAAGTGGGAGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGC\n+CTAACATGGCAAAACCCCATCTCTACTAAAAATACAAAAATTAGCCAGGCACAGTGGCTC\n+ACGCCTGTAATCTCAGCACTTTCGGAGGCCGAGGCAGGCGGATCACGAGGTGAGGAGTTC\n+GAGACCAGCCTGGCCAATGTGGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCA\n+GGCGTGATGGCGTGACCCTTTAGTCCCAGCTACTCAGGAGGCTGAGGCAGAAGAATCGCT\n+TGAACCTGGGAGGTGGAGGTTGCAGTGGGCTGAGATTGCACCACTGCATCCCAGCCTGGG\n+CGGCAGAGTGAGACTCCATCTCAAACAAACAAACAAAATTAGCCGGGCGTCGTGGTAGGC\n+ATCTATAATCCCAGCTACTAGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGTA\n+GAGGTTGCAGTGAGCTGAGATGGCGCCGCTGTACTCCAGCCTGGGTGACAGAGTGAGACA\n+CCATCTCAAACAAACAAACAAACAAACAAAATTAGCTGGGCGTTGTGGTAGGCATCTATA\n+ATCCCAGCTACTAGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCGGAGGTTG\n+CAGTGAGCCAAGATCACGCCACTGCAACAGCCTAGGCAACAGAGCAAGACTCCGTCTCAA\n+AAAAAAAAAAAAAAAGAGAGAAATAAAAATGAATTGTAAAAATGACTTCGTCTAAATGTC\n+TAAGATGAAGGAAAGGTTTCACCCATACAATTCATGCAAACTTTATTCTGCCAACTCCCC\n+AAATGCTTTATTGCTTGAAATATGTAAGTAATAACTTCAACTATCTGTGCAAGGCTGGTC\n+TTTCTGATTGTTGATAGAATATACTCAATGAATTTGTCAGTTTTAGGGGCTAAAATTTTT\n+ATTTTCTAACTCTTGCTCTGTTTAAAACAGAGGCTTTGGGATTTAAAGCACTAAAAGATC\n+CTTATGGAATCCTAAATTAA\n' |
| b |
| diff -r a88571642c6e -r 14561eb803a5 test-data/ss.her2.chr17.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ss.her2.chr17.txt Fri Oct 21 10:55:40 2016 -0400 |
| b |
| b'@@ -0,0 +1,729 @@\n+>NM_004448 Homo sapiens v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) (ERBB2), transcript variant 1, mRNA. 4624 bp, mRNA, linear, PRI 20-DEC-2004\n+Paths (1):\n+ Path 1: query 1..4624 (4624 bp) => genome 109,781..138,442 (28662 bp)\n+ cDNA direction: sense\n+ Genomic pos: 109,781..138,442 (+ strand)\n+ Number of exons: 27\n+ Coverage: 100.0 (query length: 4624 bp)\n+ Trimmed coverage: 100.0 (trimmed length: 4624 bp, trimmed region: 1..4624)\n+ Percent identity: 100.0 (4624 matches, 0 mismatches, 0 indels, 0 unknowns)\n+ Translation: 2..4006 (1334 aa)\n+ Amino acid changes: \n+\n+Alignments:\n+ Alignment for path 1:\n+\n+ 109781-110091 (1-311) 100% -> ...6678...\n+ 116770-116921 (312-463) 100% -> ...1179...\n+ 118101-118314 (464-677) 100% -> ...783...\n+ 119098-119232 (678-812) 100% -> ...360...\n+ 119593-119661 (813-881) 100% -> ...204...\n+ 119866-119981 (882-997) 100% -> ...138...\n+ 120120-120261 (998-1139) 100% -> ...1446...\n+ 121708-121827 (1140-1259) 100% -> ...274...\n+ 122102-122228 (1260-1386) 100% -> ...2837...\n+ 125066-125139 (1387-1460) 100% -> ...86...\n+ 125226-125316 (1461-1551) 100% -> ...203...\n+ 125520-125719 (1552-1751) 100% -> ...361...\n+ 126081-126213 (1752-1884) 100% -> ...81...\n+ 126295-126385 (1885-1975) 100% -> ...714...\n+ 127100-127260 (1976-2136) 100% -> ...2306...\n+ 129567-129614 (2137-2184) 100% -> ...3484...\n+ 133099-133237 (2185-2323) 100% -> ...80...\n+ 133318-133440 (2324-2446) 100% -> ...251...\n+ 133692-133790 (2447-2545) 100% -> ...715...\n+ 134506-134691 (2546-2731) 100% -> ...137...\n+ 134829-134984 (2732-2887) 100% -> ...122...\n+ 135107-135182 (2888-2963) 100% -> ...304...\n+ 135487-135633 (2964-3110) 100% -> ...708...\n+ 136342-136439 (3111-3208) 100% -> ...155...\n+ 136595-136783 (3209-3397) 100% -> ...291...\n+ 137075-137327 (3398-3650) 100% -> ...141...\n+ 137469-138442 (3651-4624) 100%\n+\n+ 0 . : . : . : . : . :\n+aa.g 1 E E V E E E G C L R K Y K N E V V\n+ 109781 GGAGGAGGTGGAGGAGGAGGGCTGCTTGAGGAAGTATAAGAATGAAGTTG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 1 GGAGGAGGTGGAGGAGGAGGGCTGCTTGAGGAAGTATAAGAATGAAGTTG\n+aa.c 1 E E V E E E G C L R K Y K N E V V\n+\n+ 50 . : . : . : . : . :\n+aa.g 18 K L R F P S I G T G E T R G A P \n+ 109831 TGAAGCTGAGATTCCCCTCCATTGGGACCGGAGAAACCAGGGGAGCCCCC\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 51 TGAAGCTGAGATTCCCCTCCATTGGGACCGGAGAAACCAGGGGAGCCCCC\n+aa.c 18 K L R F P S I G T G E T R G A P \n+\n+ 100 . : . : . : . : . :\n+aa.g 34 R A A A R P F P R G P L L R R A P \n+ 109881 CGGGCAGCCGCGCGCCCCTTCCCACGGGGCCCTTTACTGCGCCGCGCGCC\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 101 CGGGCAGCCGCGCGCCCCTTCCCACGGGGCCCTTTACTGCGCCGCGCGCC\n+aa.c 34 R A A A R P F P R G P L L R R A P \n+\n+ 150 . : . : . : . : . :\n+aa.g 51 G P H P S Q H P A P R A L P A G S\n+ 109931 CGGCCCCCACCCCTCGCAGCACCCCGCGCCCCGCGCCCTCCCAGCCGGGT\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 151 CGGCCCCCACCCCTCGCAGCACCCCGCGCCCCGCGCCCTCCCAGCCGGGT\n+aa.c 51 G P H P S Q H P A P R A L P A G S\n+\n+ 200 . : . : . : . : . :\n+aa.g 68 S R S H G A G A A V S T M E L A \n+ 109981 CCAGCCGGAGCCATGGGGCCGGAGCCGCAGTGAGCACCATGGAGCTGGCG\n+ |||||||||'..b'TTGAGTT\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 4117 CCTGCCATGCCAGGAACCTGTCCTAAGGAACCTTCCTTCCTGCTTGAGTT\n+ \n+\n+ 4400 . : . : . : . : . :\n+ \n+ 137985 CCCAGATGGCTGGAAGGGGTCCAGCCTCGTTGGAAGAGGAACAGCACTGG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 4167 CCCAGATGGCTGGAAGGGGTCCAGCCTCGTTGGAAGAGGAACAGCACTGG\n+ \n+\n+ 4450 . : . : . : . : . :\n+ \n+ 138035 GGAGTCTTTGTGGATTCTGAGGCCCTGCCCAATGAGACTCTAGGGTCCAG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 4217 GGAGTCTTTGTGGATTCTGAGGCCCTGCCCAATGAGACTCTAGGGTCCAG\n+ \n+\n+ 4500 . : . : . : . : . :\n+ \n+ 138085 TGGATGCCACAGCCCAGCTTGGCCCTTTCCTTCCAGATCCTGGGTACTGA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 4267 TGGATGCCACAGCCCAGCTTGGCCCTTTCCTTCCAGATCCTGGGTACTGA\n+ \n+\n+ 4550 . : . : . : . : . :\n+ \n+ 138135 AAGCCTTAGGGAAGCTGGCCTGAGAGGGGAAGCGGCCCTAAGGGAGTGTC\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 4317 AAGCCTTAGGGAAGCTGGCCTGAGAGGGGAAGCGGCCCTAAGGGAGTGTC\n+ \n+\n+ 4600 . : . : . : . : . :\n+ \n+ 138185 TAAGAACAAAAGCGACCCATTCAGAGACTGTCCCTGAAACCTAGTACTGC\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 4367 TAAGAACAAAAGCGACCCATTCAGAGACTGTCCCTGAAACCTAGTACTGC\n+ \n+\n+ 4650 . : . : . : . : . :\n+ \n+ 138235 CCCCCATGAGGAAGGAACAGCAATGGTGTCAGTATCCAGGCTTTGTACAG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 4417 CCCCCATGAGGAAGGAACAGCAATGGTGTCAGTATCCAGGCTTTGTACAG\n+ \n+\n+ 4700 . : . : . : . : . :\n+ \n+ 138285 AGTGCTTTTCTGTTTAGTTTTTACTTTTTTTGTTTTGTTTTTTTAAAGAT\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 4467 AGTGCTTTTCTGTTTAGTTTTTACTTTTTTTGTTTTGTTTTTTTAAAGAT\n+ \n+\n+ 4750 . : . : . : . : . :\n+ \n+ 138335 GAAATAAAGACCCAGGGGGAGAATGGGTGTTGTATGGGGAGGCAAGTGTG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 4517 GAAATAAAGACCCAGGGGGAGAATGGGTGTTGTATGGGGAGGCAAGTGTG\n+ \n+\n+ 4800 . : . : . : . : . :\n+ \n+ 138385 GGGGGTCCTTCTCCACACCCACTTTGTCCATTTGCAAATATATTTTGGAA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||\n+ 4567 GGGGGTCCTTCTCCACACCCACTTTGTCCATTTGCAAATATATTTTGGAA\n+ \n+\n+ 4850 . \n+ \n+ 138435 AACAGCTA\n+ ||||||||\n+ 4617 AACAGCTA\n+ \n+\n' |
| b |
| diff -r a88571642c6e -r 14561eb803a5 test-data/ss.her2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ss.her2.fasta Fri Oct 21 10:55:40 2016 -0400 |
| b |
| @@ -0,0 +1,79 @@ +>NM_004448 Homo sapiens v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) (ERBB2), transcript variant 1, mRNA. 4624 bp, mRNA, linear, PRI 20-DEC-2004 +GGAGGAGGTGGAGGAGGAGGGCTGCTTGAGGAAGTATAAGAATGAAGTTGTGAAGCTGAG +ATTCCCCTCCATTGGGACCGGAGAAACCAGGGGAGCCCCCCGGGCAGCCGCGCGCCCCTT +CCCACGGGGCCCTTTACTGCGCCGCGCGCCCGGCCCCCACCCCTCGCAGCACCCCGCGCC +CCGCGCCCTCCCAGCCGGGTCCAGCCGGAGCCATGGGGCCGGAGCCGCAGTGAGCACCAT +GGAGCTGGCGGCCTTGTGCCGCTGGGGGCTCCTCCTCGCCCTCTTGCCCCCCGGAGCCGC +GAGCACCCAAGTGTGCACCGGCACAGACATGAAGCTGCGGCTCCCTGCCAGTCCCGAGAC +CCACCTGGACATGCTCCGCCACCTCTACCAGGGCTGCCAGGTGGTGCAGGGAAACCTGGA +ACTCACCTACCTGCCCACCAATGCCAGCCTGTCCTTCCTGCAGGATATCCAGGAGGTGCA +GGGCTACGTGCTCATCGCTCACAACCAAGTGAGGCAGGTCCCACTGCAGAGGCTGCGGAT +TGTGCGAGGCACCCAGCTCTTTGAGGACAACTATGCCCTGGCCGTGCTAGACAATGGAGA +CCCGCTGAACAATACCACCCCTGTCACAGGGGCCTCCCCAGGAGGCCTGCGGGAGCTGCA +GCTTCGAAGCCTCACAGAGATCTTGAAAGGAGGGGTCTTGATCCAGCGGAACCCCCAGCT +CTGCTACCAGGACACGATTTTGTGGAAGGACATCTTCCACAAGAACAACCAGCTGGCTCT +CACACTGATAGACACCAACCGCTCTCGGGCCTGCCACCCCTGTTCTCCGATGTGTAAGGG +CTCCCGCTGCTGGGGAGAGAGTTCTGAGGATTGTCAGAGCCTGACGCGCACTGTCTGTGC +CGGTGGCTGTGCCCGCTGCAAGGGGCCACTGCCCACTGACTGCTGCCATGAGCAGTGTGC +TGCCGGCTGCACGGGCCCCAAGCACTCTGACTGCCTGGCCTGCCTCCACTTCAACCACAG +TGGCATCTGTGAGCTGCACTGCCCAGCCCTGGTCACCTACAACACAGACACGTTTGAGTC +CATGCCCAATCCCGAGGGCCGGTATACATTCGGCGCCAGCTGTGTGACTGCCTGTCCCTA +CAACTACCTTTCTACGGACGTGGGATCCTGCACCCTCGTCTGCCCCCTGCACAACCAAGA +GGTGACAGCAGAGGATGGAACACAGCGGTGTGAGAAGTGCAGCAAGCCCTGTGCCCGAGT +GTGCTATGGTCTGGGCATGGAGCACTTGCGAGAGGTGAGGGCAGTTACCAGTGCCAATAT +CCAGGAGTTTGCTGGCTGCAAGAAGATCTTTGGGAGCCTGGCATTTCTGCCGGAGAGCTT +TGATGGGGACCCAGCCTCCAACACTGCCCCGCTCCAGCCAGAGCAGCTCCAAGTGTTTGA +GACTCTGGAAGAGATCACAGGTTACCTATACATCTCAGCATGGCCGGACAGCCTGCCTGA +CCTCAGCGTCTTCCAGAACCTGCAAGTAATCCGGGGACGAATTCTGCACAATGGCGCCTA +CTCGCTGACCCTGCAAGGGCTGGGCATCAGCTGGCTGGGGCTGCGCTCACTGAGGGAACT +GGGCAGTGGACTGGCCCTCATCCACCATAACACCCACCTCTGCTTCGTGCACACGGTGCC +CTGGGACCAGCTCTTTCGGAACCCGCACCAAGCTCTGCTCCACACTGCCAACCGGCCAGA +GGACGAGTGTGTGGGCGAGGGCCTGGCCTGCCACCAGCTGTGCGCCCGAGGGCACTGCTG +GGGTCCAGGGCCCACCCAGTGTGTCAACTGCAGCCAGTTCCTTCGGGGCCAGGAGTGCGT +GGAGGAATGCCGAGTACTGCAGGGGCTCCCCAGGGAGTATGTGAATGCCAGGCACTGTTT +GCCGTGCCACCCTGAGTGTCAGCCCCAGAATGGCTCAGTGACCTGTTTTGGACCGGAGGC +TGACCAGTGTGTGGCCTGTGCCCACTATAAGGACCCTCCCTTCTGCGTGGCCCGCTGCCC +CAGCGGTGTGAAACCTGACCTCTCCTACATGCCCATCTGGAAGTTTCCAGATGAGGAGGG +CGCATGCCAGCCTTGCCCCATCAACTGCACCCACTCCTGTGTGGACCTGGATGACAAGGG +CTGCCCCGCCGAGCAGAGAGCCAGCCCTCTGACGTCCATCATCTCTGCGGTGGTTGGCAT +TCTGCTGGTCGTGGTCTTGGGGGTGGTCTTTGGGATCCTCATCAAGCGACGGCAGCAGAA +GATCCGGAAGTACACGATGCGGAGACTGCTGCAGGAAACGGAGCTGGTGGAGCCGCTGAC +ACCTAGCGGAGCGATGCCCAACCAGGCGCAGATGCGGATCCTGAAAGAGACGGAGCTGAG +GAAGGTGAAGGTGCTTGGATCTGGCGCTTTTGGCACAGTCTACAAGGGCATCTGGATCCC +TGATGGGGAGAATGTGAAAATTCCAGTGGCCATCAAAGTGTTGAGGGAAAACACATCCCC +CAAAGCCAACAAAGAAATCTTAGACGAAGCATACGTGATGGCTGGTGTGGGCTCCCCATA +TGTCTCCCGCCTTCTGGGCATCTGCCTGACATCCACGGTGCAGCTGGTGACACAGCTTAT +GCCCTATGGCTGCCTCTTAGACCATGTCCGGGAAAACCGCGGACGCCTGGGCTCCCAGGA +CCTGCTGAACTGGTGTATGCAGATTGCCAAGGGGATGAGCTACCTGGAGGATGTGCGGCT +CGTACACAGGGACTTGGCCGCTCGGAACGTGCTGGTCAAGAGTCCCAACCATGTCAAAAT +TACAGACTTCGGGCTGGCTCGGCTGCTGGACATTGACGAGACAGAGTACCATGCAGATGG +GGGCAAGGTGCCCATCAAGTGGATGGCGCTGGAGTCCATTCTCCGCCGGCGGTTCACCCA +CCAGAGTGATGTGTGGAGTTATGGTGTGACTGTGTGGGAGCTGATGACTTTTGGGGCCAA +ACCTTACGATGGGATCCCAGCCCGGGAGATCCCTGACCTGCTGGAAAAGGGGGAGCGGCT +GCCCCAGCCCCCCATCTGCACCATTGATGTCTACATGATCATGGTCAAATGTTGGATGAT +TGACTCTGAATGTCGGCCAAGATTCCGGGAGTTGGTGTCTGAATTCTCCCGCATGGCCAG +GGACCCCCAGCGCTTTGTGGTCATCCAGAATGAGGACTTGGGCCCAGCCAGTCCCTTGGA +CAGCACCTTCTACCGCTCACTGCTGGAGGACGATGACATGGGGGACCTGGTGGATGCTGA +GGAGTATCTGGTACCCCAGCAGGGCTTCTTCTGTCCAGACCCTGCCCCGGGCGCTGGGGG +CATGGTCCACCACAGGCACCGCAGCTCATCTACCAGGAGTGGCGGTGGGGACCTGACACT +AGGGCTGGAGCCCTCTGAAGAGGAGGCCCCCAGGTCTCCACTGGCACCCTCCGAAGGGGC +TGGCTCCGATGTATTTGATGGTGACCTGGGAATGGGGGCAGCCAAGGGGCTGCAAAGCCT +CCCCACACATGACCCCAGCCCTCTACAGCGGTACAGTGAGGACCCCACAGTACCCCTGCC +CTCTGAGACTGATGGCTACGTTGCCCCCCTGACCTGCAGCCCCCAGCCTGAATATGTGAA +CCAGCCAGATGTTCGGCCCCAGCCCCCTTCGCCCCGAGAGGGCCCTCTGCCTGCTGCCCG +ACCTGCTGGTGCCACTCTGGAAAGGCCCAAGACTCTCTCCCCAGGGAAGAATGGGGTCGT +CAAAGACGTTTTTGCCTTTGGGGGTGCCGTGGAGAACCCCGAGTACTTGACACCCCAGGG +AGGAGCTGCCCCTCAGCCCCACCCTCCTCCTGCCTTCAGCCCAGCCTTCGACAACCTCTA +TTACTGGGACCAGGACCCACCAGAGCGGGGGGCTCCACCCAGCACCTTCAAAGGGACACC +TACGGCAGAGAACCCAGAGTACCTGGGTCTGGACGTGCCAGTGTGAACCAGAAGGCCAAG +TCCGCAGAAGCCCTGATGTGTCCTCAGGGAGCAGGGAAGGCCTGACTTCTGCTGGCATCA +AGAGGTGGGAGGGCCCTCCGACCACTTCCAGGGGAACCTGCCATGCCAGGAACCTGTCCT +AAGGAACCTTCCTTCCTGCTTGAGTTCCCAGATGGCTGGAAGGGGTCCAGCCTCGTTGGA +AGAGGAACAGCACTGGGGAGTCTTTGTGGATTCTGAGGCCCTGCCCAATGAGACTCTAGG +GTCCAGTGGATGCCACAGCCCAGCTTGGCCCTTTCCTTCCAGATCCTGGGTACTGAAAGC +CTTAGGGAAGCTGGCCTGAGAGGGGAAGCGGCCCTAAGGGAGTGTCTAAGAACAAAAGCG +ACCCATTCAGAGACTGTCCCTGAAACCTAGTACTGCCCCCCATGAGGAAGGAACAGCAAT +GGTGTCAGTATCCAGGCTTTGTACAGAGTGCTTTTCTGTTTAGTTTTTACTTTTTTTGTT +TTGTTTTTTTAAAGATGAAATAAAGACCCAGGGGGAGAATGGGTGTTGTATGGGGAGGCA +AGTGTGGGGGGTCCTTCTCCACACCCACTTTGTCCATTTGCAAATATATTTTGGAAAACA +GCTA |
| b |
| diff -r a88571642c6e -r 14561eb803a5 tool-data/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Fri Oct 21 10:55:40 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="gmap_indices_for_uid" comment_char="#" allow_duplicate_entries="False"> + <columns>uid, dbkey, name, kmers, maps, snps, value</columns> + <file path="tool-data/gmap_indices.loc" /> + </table> +</tables> \ No newline at end of file |
| b |
| diff -r a88571642c6e -r 14561eb803a5 tool_dependencies.xml --- a/tool_dependencies.xml Wed Sep 28 10:49:02 2016 -0400 +++ b/tool_dependencies.xml Fri Oct 21 10:55:40 2016 -0400 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="gmap" version="2013-05-09"> - <repository changeset_revision="8bacc25e2023" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="f59058e92ed7" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |