1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/18c426204a33/
changeset: 18c426204a33
user: jgoecks
date: 2012-04-23 17:24:46
summary: Better message when creating a custom build.
affected #: 1 file
diff -r ebd5932ed7f1d0b434383995ea1338609b9814f4 -r 18c426204a337f94377074afa863261b6a4b10be templates/user/dbkeys.mako
--- a/templates/user/dbkeys.mako
+++ b/templates/user/dbkeys.mako
@@ -149,7 +149,7 @@
% if 'count' in dct:
${dct['count']}
% else:
- ?
+ Processing
% endif
</td><td><form action="dbkeys" method="post"><input type="hidden" name="key" value="${key}" /><input type="submit" name="delete" value="Delete" /></form></td>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/8b773372d0dc/
changeset: 8b773372d0dc
user: dan
date: 2012-04-23 12:42:19
summary: Partial revert for c32b71dcfc84.
affected #: 1 file
diff -r d7fecd64a8027af7872e125d6772d3a04f5e1973 -r 8b773372d0dce1d815b90d257efa073d5a039e72 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1125,7 +1125,7 @@
return ldda
def clear_associated_files( self, metadata_safe = False, purge = False ):
# metadata_safe = True means to only clear when assoc.metadata_safe == False
- for assoc in self.implicitly_converted_datasets + self.implicitly_converted_parent_datasets:
+ for assoc in self.implicitly_converted_datasets:
if not metadata_safe or not assoc.metadata_safe:
assoc.clear( purge = purge )
def get_display_name( self ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/d7fecd64a802/
changeset: d7fecd64a802
user: jgoecks
date: 2012-04-22 17:58:24
summary: Refactor and simply tophat wrapper.
affected #: 2 files
diff -r 47bcf28a53e982e5c3062218f0eb8a9d24c6cbd6 -r d7fecd64a8027af7872e125d6772d3a04f5e1973 tools/ngs_rna/tophat_wrapper.py
--- a/tools/ngs_rna/tophat_wrapper.py
+++ b/tools/ngs_rna/tophat_wrapper.py
@@ -171,7 +171,7 @@
opts += ' --no-coverage-search'
if options.microexon_search:
opts += ' --microexon-search'
- if options.single_paired == 'paired':
+ if options.single_paired == 'paired' and options.mate_std_dev:
opts += ' --mate-std-dev %s' % options.mate_std_dev
if options.seg_mismatches:
opts += ' --segment-mismatches %d' % int( options.seg_mismatches )
diff -r 47bcf28a53e982e5c3062218f0eb8a9d24c6cbd6 -r d7fecd64a8027af7872e125d6772d3a04f5e1973 tools/ngs_rna/tophat_wrapper.xml
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -7,132 +7,100 @@
</requirements><command interpreter="python">
tophat_wrapper.py
- ## Change this to accommodate the number of threads you have available.
- --num-threads="4"
+
+ ## Change this to accommodate the number of threads you have available.
+ --num-threads="4"
- ## Provide outputs.
- --junctions-output=$junctions
- --hits-output=$accepted_hits
+ ## Provide outputs.
+ --junctions-output=$junctions
+ --hits-output=$accepted_hits
- ## Handle reference file.
- #if $refGenomeSource.genomeSource == "history":
- --own-file=$refGenomeSource.ownFile
+ ## Handle reference file.
+ #if $refGenomeSource.genomeSource == "history":
+ --own-file=$refGenomeSource.ownFile
+ #else:
+ --indexes-path="${refGenomeSource.index.fields.path}"
+ #end if
+
+ ## Are reads single-end or paired?
+ --single-paired=$singlePaired.sPaired
+
+ ## First input file always required.
+ --input1=$input1
+
+ ## Second input only if input is paired-end.
+ #if $singlePaired.sPaired == "paired"
+ --input2=$singlePaired.input2
+ -r $singlePaired.mate_inner_distance
+ --mate-std-dev=$singlePaired.mate_std_dev
+ #end if
+
+ ## Set params.
+ --settings=$params.settingsType
+ #if $params.settingsType == "full":
+ -a $params.anchor_length
+ -m $params.splice_mismatches
+ -i $params.min_intron_length
+ -I $params.max_intron_length
+ -g $params.max_multihits
+ --min-segment-intron $params.min_segment_intron
+ --max-segment-intron $params.max_segment_intron
+ --seg-mismatches=$params.seg_mismatches
+ --seg-length=$params.seg_length
+ --library-type=$params.library_type
+
+ ## Indel search.
+ #if $params.indel_search.allow_indel_search == "Yes":
+ ## --allow-indels
+ --max-insertion-length $params.indel_search.max_insertion_length
+ --max-deletion-length $params.indel_search.max_deletion_length
#else:
- --indexes-path="${refGenomeSource.index.fields.path}"
+ --no-novel-indels
#end if
- ## Are reads single-end or paired?
- --single-paired=$singlePaired.sPaired
-
- ## First input file always required.
- --input1=$input1
-
- ## Set params based on whether reads are single-end or paired.
- #if $singlePaired.sPaired == "single":
- --settings=$singlePaired.sParams.sSettingsType
- #if $singlePaired.sParams.sSettingsType == "full":
- -a $singlePaired.sParams.anchor_length
- -m $singlePaired.sParams.splice_mismatches
- -i $singlePaired.sParams.min_intron_length
- -I $singlePaired.sParams.max_intron_length
- -g $singlePaired.sParams.max_multihits
- --min-segment-intron $singlePaired.sParams.min_segment_intron
- --max-segment-intron $singlePaired.sParams.max_segment_intron
- --seg-mismatches=$singlePaired.sParams.seg_mismatches
- --seg-length=$singlePaired.sParams.seg_length
- --library-type=$singlePaired.sParams.library_type
-
- ## Indel search.
- #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes":
- ## --allow-indels
- --max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length
- --max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length
- #else:
- --no-novel-indels
- #end if
-
- ## Supplying junctions parameters.
- #if $singlePaired.sParams.own_junctions.use_junctions == "Yes":
- #if $singlePaired.sParams.own_junctions.gene_model_ann.use_annotations == "Yes":
- -G $singlePaired.sParams.own_junctions.gene_model_ann.gene_annotation_model
- #end if
- #if $singlePaired.sParams.own_junctions.raw_juncs.use_juncs == "Yes":
- -j $singlePaired.sParams.own_junctions.raw_juncs.raw_juncs
- #end if
- ## TODO: No idea why a string cast is necessary, but it is:
- #if str($singlePaired.sParams.own_junctions.no_novel_juncs) == "Yes":
- --no-novel-juncs
- #end if
- #end if
-
- #if $singlePaired.sParams.coverage_search.use_search == "Yes":
- --coverage-search
- --min-coverage-intron $singlePaired.sParams.coverage_search.min_coverage_intron
- --max-coverage-intron $singlePaired.sParams.coverage_search.max_coverage_intron
- #else:
- --no-coverage-search
- #end if
- ## TODO: No idea why the type conversion is necessary, but it seems to be.
- #if str($singlePaired.sParams.microexon_search) == "Yes":
- --microexon-search
- #end if
+ ## Supplying junctions parameters.
+ #if $params.own_junctions.use_junctions == "Yes":
+ #if $params.own_junctions.gene_model_ann.use_annotations == "Yes":
+ -G $params.own_junctions.gene_model_ann.gene_annotation_model
#end if
- #else:
- --input2=$singlePaired.input2
- -r $singlePaired.mate_inner_distance
- --settings=$singlePaired.pParams.pSettingsType
- #if $singlePaired.pParams.pSettingsType == "full":
- --mate-std-dev=$singlePaired.pParams.mate_std_dev
- -a $singlePaired.pParams.anchor_length
- -m $singlePaired.pParams.splice_mismatches
- -i $singlePaired.pParams.min_intron_length
- -I $singlePaired.pParams.max_intron_length
- -g $singlePaired.pParams.max_multihits
- --min-segment-intron $singlePaired.pParams.min_segment_intron
- --max-segment-intron $singlePaired.pParams.max_segment_intron
- --seg-mismatches=$singlePaired.pParams.seg_mismatches
- --seg-length=$singlePaired.pParams.seg_length
- --library-type=$singlePaired.pParams.library_type
-
- ## Indel search.
- #if $singlePaired.pParams.indel_search.allow_indel_search == "Yes":
- ## --allow-indels
- --max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length
- --max-deletion-length $singlePaired.pParams.indel_search.max_deletion_length
- #else:
- --no-novel-indels
- #end if
-
- ## Supplying junctions parameters.
- #if $singlePaired.pParams.own_junctions.use_junctions == "Yes":
- #if $singlePaired.pParams.own_junctions.gene_model_ann.use_annotations == "Yes":
- -G $singlePaired.pParams.own_junctions.gene_model_ann.gene_annotation_model
- #end if
- #if $singlePaired.pParams.own_junctions.raw_juncs.use_juncs == "Yes":
- -j $singlePaired.pParams.own_junctions.raw_juncs.raw_juncs
- #end if
- ## TODO: No idea why type cast is necessary, but it is:
- #if str($singlePaired.pParams.own_junctions.no_novel_juncs) == "Yes":
- --no-novel-juncs
- #end if
- #end if
-
- #if $singlePaired.pParams.coverage_search.use_search == "Yes":
- --coverage-search
- --min-coverage-intron $singlePaired.pParams.coverage_search.min_coverage_intron
- --max-coverage-intron $singlePaired.pParams.coverage_search.max_coverage_intron
- #else:
- --no-coverage-search
- #end if
- ## TODO: No idea why the type conversion is necessary, but it seems to be.
- #if str ($singlePaired.pParams.microexon_search) == "Yes":
- --microexon-search
- #end if
+ #if $params.own_junctions.raw_juncs.use_juncs == "Yes":
+ -j $params.own_junctions.raw_juncs.raw_juncs
+ #end if
+ ## TODO: No idea why a string cast is necessary, but it is:
+ #if str($params.own_junctions.no_novel_juncs) == "Yes":
+ --no-novel-juncs
#end if
#end if
+
+ #if $params.coverage_search.use_search == "Yes":
+ --coverage-search
+ --min-coverage-intron $params.coverage_search.min_coverage_intron
+ --max-coverage-intron $params.coverage_search.max_coverage_intron
+ #else:
+ --no-coverage-search
+ #end if
+ ## TODO: No idea why the type conversion is necessary, but it seems to be.
+ #if str($params.microexon_search) == "Yes":
+ --microexon-search
+ #end if
+ #end if
</command><inputs>
- <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
+ <conditional name="singlePaired">
+ <param name="sPaired" type="select" label="Is this library mate-paired?">
+ <option value="single">Single-end</option>
+ <option value="paired">Paired-end</option>
+ </param>
+ <when value="single">
+ <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
+ </when>
+ <when value="paired">
+ <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
+ <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
+ <param name="mate_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs" />
+ <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/>
+ </when>
+ </conditional><conditional name="refGenomeSource"><param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"><option value="indexed">Use a built-in index</option>
@@ -150,193 +118,94 @@
<param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /></when><!-- history --></conditional><!-- refGenomeSource -->
- <conditional name="singlePaired">
- <param name="sPaired" type="select" label="Is this library mate-paired?">
- <option value="single">Single-end</option>
- <option value="paired">Paired-end</option>
+ <conditional name="params">
+ <param name="settingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters.">
+ <option value="preSet">Use Defaults</option>
+ <option value="full">Full parameter list</option></param>
- <when value="single">
- <conditional name="sParams">
- <param name="sSettingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters.">
- <option value="preSet">Use Defaults</option>
- <option value="full">Full parameter list</option>
- </param>
- <when value="preSet" />
- <!-- Full/advanced params. -->
- <when value="full">
- <param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.">
- <option value="fr-unstranded">FR Unstranded</option>
- <option value="fr-firststrand">FR First Strand</option>
- <option value="fr-secondstrand">FR Second Strand</option>
+ <when value="preSet" />
+ <!-- Full/advanced params. -->
+ <when value="full">
+ <param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.">
+ <option value="fr-unstranded">FR Unstranded</option>
+ <option value="fr-firststrand">FR First Strand</option>
+ <option value="fr-secondstrand">FR Second Strand</option>
+ </param>
+ <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." />
+ <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
+ <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
+ <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
+ <conditional name="indel_search">
+ <param name="allow_indel_search" type="select" label="Allow indel search">
+ <option value="Yes">Yes</option>
+ <option value="No">No</option></param>
- <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." />
- <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
- <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
- <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
- <conditional name="indel_search">
- <param name="allow_indel_search" type="select" label="Allow indel search">
- <option value="Yes">Yes</option>
- <option value="No">No</option>
- </param>
- <when value="No"/>
- <when value="Yes">
- <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
- <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
- </when>
- </conditional>
-alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
- <param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />
- <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
- <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
- <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
- <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
-
- <!-- Options for supplying own junctions. -->
- <conditional name="own_junctions">
- <param name="use_junctions" type="select" label="Use Own Junctions">
+ <when value="No"/>
+ <when value="Yes">
+ <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
+ <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
+ </when>
+ </conditional>
+ alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
+ <param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />
+ <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
+ <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
+ <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
+ <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
+
+ <!-- Options for supplying own junctions. -->
+ <conditional name="own_junctions">
+ <param name="use_junctions" type="select" label="Use Own Junctions">
+ <option value="No">No</option>
+ <option value="Yes">Yes</option>
+ </param>
+ <when value="Yes">
+ <conditional name="gene_model_ann">
+ <param name="use_annotations" type="select" label="Use Gene Annotation Model">
+ <option value="No">No</option>
+ <option value="Yes">Yes</option>
+ </param>
+ <when value="No" />
+ <when value="Yes">
+ <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
+ </when>
+ </conditional>
+ <conditional name="raw_juncs">
+ <param name="use_juncs" type="select" label="Use Raw Junctions">
+ <option value="No">No</option>
+ <option value="Yes">Yes</option>
+ </param>
+ <when value="No" />
+ <when value="Yes">
+ <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
+ </when>
+ </conditional>
+ <param name="no_novel_juncs" type="select" label="Only look for supplied junctions"><option value="No">No</option><option value="Yes">Yes</option></param>
- <when value="Yes">
- <conditional name="gene_model_ann">
- <param name="use_annotations" type="select" label="Use Gene Annotation Model">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
- </param>
- <when value="No" />
- <when value="Yes">
- <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
- </when>
- </conditional>
- <conditional name="raw_juncs">
- <param name="use_juncs" type="select" label="Use Raw Junctions">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
- </param>
- <when value="No" />
- <when value="Yes">
- <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
- </when>
- </conditional>
- <param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
- </param>
- </when>
- <when value="No" />
- </conditional><!-- /own_junctions -->
-
- <!-- Coverage search. -->
- <conditional name="coverage_search">
- <param name="use_search" type="select" label="Use Coverage Search">
- <option selected="true" value="Yes">Yes</option>
- <option value="No">No</option>
- </param>
- <when value="Yes">
- <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />
- <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" />
- </when>
- <when value="No" />
- </conditional>
- <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.">
+ </when>
+ <when value="No" />
+ </conditional><!-- /own_junctions -->
+
+ <!-- Coverage search. -->
+ <conditional name="coverage_search">
+ <param name="use_search" type="select" label="Use Coverage Search">
+ <option selected="true" value="Yes">Yes</option><option value="No">No</option>
- <option value="Yes">Yes</option>
- </param>
- </when><!-- full -->
- </conditional><!-- sParams -->
- </when><!-- single -->
- <when value="paired">
- <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
- <param name="mate_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs" />
- <conditional name="pParams">
- <param name="pSettingsType" type="select" label="TopHat settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
- <option value="preSet">Commonly used</option>
- <option value="full">Full parameter list</option></param>
- <when value="preSet" />
- <!-- Full/advanced params. -->
- <when value="full">
- <param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.">
- <option value="fr-unstranded">FR Unstranded</option>
- <option value="fr-firststrand">FR First Strand</option>
- <option value="fr-secondstrand">FR Second Strand</option>
- </param>
- <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/>
- <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." />
- <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
- <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
- <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
- <conditional name="indel_search">
- <param name="allow_indel_search" type="select" label="Allow indel search">
- <option value="Yes">Yes</option>
- <option value="No">No</option>
- </param>
- <when value="No"/>
- <when value="Yes">
- <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
- <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
- </when>
- </conditional>
- <param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />
- <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
- <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
- <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
- <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
- <!-- Options for supplying own junctions. -->
- <conditional name="own_junctions">
- <param name="use_junctions" type="select" label="Use Own Junctions">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
- </param>
- <when value="Yes">
- <conditional name="gene_model_ann">
- <param name="use_annotations" type="select" label="Use Gene Annotation Model">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
- </param>
- <when value="No" />
- <when value="Yes">
- <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
- </when>
- </conditional>
- <conditional name="raw_juncs">
- <param name="use_juncs" type="select" label="Use Raw Junctions">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
- </param>
- <when value="No" />
- <when value="Yes">
- <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
- </when>
- </conditional>
- <param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
- </param>
- </when>
- <when value="No" />
- </conditional><!-- /own_junctions -->
-
- <!-- Coverage search. -->
- <conditional name="coverage_search">
- <param name="use_search" type="select" label="Use Coverage Search">
- <option selected="true" value="Yes">Yes</option>
- <option value="No">No</option>
- </param>
- <when value="Yes">
- <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />
- <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" />
- </when>
- <when value="No" />
- </conditional>
- <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
- </param>
- </when><!-- full -->
- </conditional><!-- pParams -->
- </when><!-- paired -->
- </conditional>
+ <when value="Yes">
+ <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />
+ <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" />
+ </when>
+ <when value="No" />
+ </conditional>
+ <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.">
+ <option value="No">No</option>
+ <option value="Yes">Yes</option>
+ </param>
+ </when><!-- full -->
+ </conditional><!-- params --></inputs><outputs>
@@ -425,11 +294,11 @@
tophat -o tmp_dir -p 1 tophat_in1 test-data/tophat_in2.fastqsanger
Rename the files in tmp_dir appropriately
-->
+ <param name="sPaired" value="single" /><param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /><param name="genomeSource" value="indexed" /><param name="index" value="tophat_test" />
- <param name="sPaired" value="single" />
- <param name="sSettingsType" value="preSet" />
+ <param name="settingsType" value="preSet" /><output name="junctions" file="tophat_out1j.bed" /><output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" /></test>
@@ -440,13 +309,13 @@
tophat -o tmp_dir -p 1 -r 20 tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
Rename the files in tmp_dir appropriately
-->
+ <param name="sPaired" value="paired" /><param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
+ <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" /><param name="genomeSource" value="history" /><param name="ownFile" ftype="fasta" value="tophat_in1.fasta" />
- <param name="sPaired" value="paired" />
- <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" /><param name="mate_inner_distance" value="20" />
- <param name="pSettingsType" value="preSet" />
+ <param name="settingsType" value="preSet" /><output name="junctions" file="tophat_out2j.bed" /><output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" /></test>
@@ -458,11 +327,11 @@
Replace the + with double-dash
Rename the files in tmp_dir appropriately
-->
+ <param name="sPaired" value="single"/><param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/><param name="genomeSource" value="history"/><param name="ownFile" value="tophat_in1.fasta"/>
- <param name="sPaired" value="single"/>
- <param name="sSettingsType" value="full"/>
+ <param name="settingsType" value="full"/><param name="library_type" value="FR Unstranded"/><param name="anchor_length" value="8"/><param name="splice_mismatches" value="0"/>
@@ -496,13 +365,13 @@
Replace the + with double-dash
Rename the files in tmp_dir appropriately
-->
+ <param name="sPaired" value="paired"/><param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
+ <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/><param name="genomeSource" value="indexed"/><param name="index" value="tophat_test"/>
- <param name="sPaired" value="paired"/>
- <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/><param name="mate_inner_distance" value="20"/>
- <param name="pSettingsType" value="full"/>
+ <param name="settingsType" value="full"/><param name="library_type" value="FR Unstranded"/><param name="mate_std_dev" value="20"/><param name="anchor_length" value="8"/>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/49195c2f37ce/
changeset: 49195c2f37ce
user: greg
date: 2012-04-21 03:27:34
summary: Fixes for setting repository metadata on older change sets in a tool shed repository.
affected #: 2 files
diff -r 6f7240344304a143a3d70182092c61931595b613 -r 49195c2f37cedabd034984b08058b163302286f0 lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -401,10 +401,14 @@
fh.close()
if not ( check_binary( tmp_filename ) or check_image( tmp_filename ) or check_gzip( tmp_filename )[ 0 ]
or check_bz2( tmp_filename )[ 0 ] or check_zip( tmp_filename ) ):
- # Make sure we're looking at a tool config and not a display application config or something else.
- element_tree = util.parse_xml( tmp_filename )
- element_tree_root = element_tree.getroot()
- if element_tree_root.tag == 'tool':
+ try:
+ # Make sure we're looking at a tool config and not a display application config or something else.
+ element_tree = util.parse_xml( tmp_filename )
+ element_tree_root = element_tree.getroot()
+ is_tool = element_tree_root.tag == 'tool'
+ except:
+ is_tool = False
+ if is_tool:
try:
tool = load_tool( trans, tmp_filename )
valid = True
diff -r 6f7240344304a143a3d70182092c61931595b613 -r 49195c2f37cedabd034984b08058b163302286f0 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -919,10 +919,14 @@
fh.close()
if not ( check_binary( tmp_filename ) or check_image( tmp_filename ) or check_gzip( tmp_filename )[ 0 ]
or check_bz2( tmp_filename )[ 0 ] or check_zip( tmp_filename ) ):
- # Make sure we're looking at a tool config and not a display application config or something else.
- element_tree = util.parse_xml( tmp_filename )
- element_tree_root = element_tree.getroot()
- if element_tree_root.tag == 'tool':
+ try:
+ # Make sure we're looking at a tool config and not a display application config or something else.
+ element_tree = util.parse_xml( tmp_filename )
+ element_tree_root = element_tree.getroot()
+ is_tool = element_tree_root.tag == 'tool'
+ except:
+ is_tool = False
+ if is_tool:
try:
tool = load_tool( trans, tmp_filename )
valid = True
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/6af88237056f/
changeset: 6af88237056f
user: jgoecks
date: 2012-04-20 23:08:55
summary: Basic support for Tophat2.
affected #: 4 files
diff -r 89786a8d42c1fbbfa84bfcbab07702a942d57d1b -r 6af88237056f0d4c7ae4c3dd5af647cde4830710 test-data/tophat_out2j.bed
--- a/test-data/tophat_out2j.bed
+++ b/test-data/tophat_out2j.bed
@@ -1,3 +1,3 @@
track name=junctions description="TopHat junctions"
-test_chromosome 179 400 JUNC00000001 38 + 179 400 255,0,0 2 71,50 0,171
-test_chromosome 350 549 JUNC00000002 30 + 350 549 255,0,0 2 50,49 0,150
+test_chromosome 179 400 JUNC00000001 45 + 179 400 255,0,0 2 71,50 0,171
+test_chromosome 350 550 JUNC00000002 38 + 350 550 255,0,0 2 50,50 0,150
diff -r 89786a8d42c1fbbfa84bfcbab07702a942d57d1b -r 6af88237056f0d4c7ae4c3dd5af647cde4830710 test-data/tophat_out4j.bed
--- a/test-data/tophat_out4j.bed
+++ b/test-data/tophat_out4j.bed
@@ -1,3 +1,3 @@
track name=junctions description="TopHat junctions"
-test_chromosome 179 400 JUNC00000001 38 + 179 400 255,0,0 2 71,50 0,171
-test_chromosome 350 549 JUNC00000002 30 + 350 549 255,0,0 2 50,49 0,150
+test_chromosome 179 400 JUNC00000001 45 + 179 400 255,0,0 2 71,50 0,171
+test_chromosome 350 550 JUNC00000002 38 + 350 550 255,0,0 2 50,50 0,150
diff -r 89786a8d42c1fbbfa84bfcbab07702a942d57d1b -r 6af88237056f0d4c7ae4c3dd5af647cde4830710 tools/ngs_rna/tophat_wrapper.py
--- a/tools/ngs_rna/tophat_wrapper.py
+++ b/tools/ngs_rna/tophat_wrapper.py
@@ -28,7 +28,6 @@
parser.add_option( '-I', '--max-intron-length', dest='max_intron_length',
help='The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read.' )
parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' )
- parser.add_option( '', '--initial-read-mismatches', dest='initial_read_mismatches', help='Number of mismatches allowed in the initial read mapping' )
parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' )
parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' )
parser.add_option( '', '--library-type', dest='library_type', help='TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.' )
@@ -53,15 +52,10 @@
parser.add_option( '', '--no-novel-indels', action="store_true", dest='no_novel_indels', help="Skip indel search. Indel search is enabled by default.")
# Types of search.
parser.add_option( '', '--microexon-search', action="store_true", dest='microexon_search', help='With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.')
- parser.add_option( '', '--closure-search', action="store_true", dest='closure_search', help='Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (<= 50bp)')
- parser.add_option( '', '--no-closure-search', action="store_false", dest='closure_search' )
parser.add_option( '', '--coverage-search', action="store_true", dest='coverage_search', help='Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.')
parser.add_option( '', '--no-coverage-search', action="store_false", dest='coverage_search' )
parser.add_option( '', '--min-segment-intron', dest='min_segment_intron', help='Minimum intron length that may be found during split-segment search' )
parser.add_option( '', '--max-segment-intron', dest='max_segment_intron', help='Maximum intron length that may be found during split-segment search' )
- parser.add_option( '', '--min-closure-exon', dest='min_closure_exon', help='Minimum length for exonic hops in potential splice graph' )
- parser.add_option( '', '--min-closure-intron', dest='min_closure_intron', help='Minimum intron length that may be found during closure search' )
- parser.add_option( '', '--max-closure-intron', dest='max_closure_intron', help='Maximum intron length that may be found during closure search' )
parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' )
parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' )
@@ -175,16 +169,10 @@
opts += ' --coverage-search --min-coverage-intron %s --max-coverage-intron %s' % ( options.min_coverage_intron, options.max_coverage_intron )
else:
opts += ' --no-coverage-search'
- if options.closure_search:
- opts += ' --closure-search --min-closure-exon %s --min-closure-intron %s --max-closure-intron %s' % ( options.min_closure_exon, options.min_closure_intron, options.max_closure_intron )
- else:
- opts += ' --no-closure-search'
if options.microexon_search:
opts += ' --microexon-search'
if options.single_paired == 'paired':
opts += ' --mate-std-dev %s' % options.mate_std_dev
- if options.initial_read_mismatches:
- opts += ' --initial-read-mismatches %d' % int( options.initial_read_mismatches )
if options.seg_mismatches:
opts += ' --segment-mismatches %d' % int( options.seg_mismatches )
if options.seg_length:
diff -r 89786a8d42c1fbbfa84bfcbab07702a942d57d1b -r 6af88237056f0d4c7ae4c3dd5af647cde4830710 tools/ngs_rna/tophat_wrapper.xml
--- a/tools/ngs_rna/tophat_wrapper.xml
+++ b/tools/ngs_rna/tophat_wrapper.xml
@@ -1,5 +1,5 @@
<tool id="tophat" name="Tophat for Illumina" version="0.5">
- <!-- Wrapper compatible with Tophat versions 1.3.0 to 1.4.1 -->
+ <!-- Wrapper compatible with Tophat versions 1.3.0 to 2.0.0 --><description>Find splice junctions using RNA-seq data</description><version_command>tophat --version</version_command><requirements>
@@ -38,7 +38,6 @@
-g $singlePaired.sParams.max_multihits
--min-segment-intron $singlePaired.sParams.min_segment_intron
--max-segment-intron $singlePaired.sParams.max_segment_intron
- --initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches
--seg-mismatches=$singlePaired.sParams.seg_mismatches
--seg-length=$singlePaired.sParams.seg_length
--library-type=$singlePaired.sParams.library_type
@@ -66,14 +65,6 @@
#end if
#end if
- #if $singlePaired.sParams.closure_search.use_search == "Yes":
- --closure-search
- --min-closure-exon $singlePaired.sParams.closure_search.min_closure_exon
- --min-closure-intron $singlePaired.sParams.closure_search.min_closure_intron
- --max-closure-intron $singlePaired.sParams.closure_search.max_closure_intron
- #else:
- --no-closure-search
- #end if
#if $singlePaired.sParams.coverage_search.use_search == "Yes":
--coverage-search
--min-coverage-intron $singlePaired.sParams.coverage_search.min_coverage_intron
@@ -99,7 +90,6 @@
-g $singlePaired.pParams.max_multihits
--min-segment-intron $singlePaired.pParams.min_segment_intron
--max-segment-intron $singlePaired.pParams.max_segment_intron
- --initial-read-mismatches=$singlePaired.pParams.initial_read_mismatches
--seg-mismatches=$singlePaired.pParams.seg_mismatches
--seg-length=$singlePaired.pParams.seg_length
--library-type=$singlePaired.pParams.library_type
@@ -127,14 +117,6 @@
#end if
#end if
- #if $singlePaired.pParams.closure_search.use_search == "Yes":
- --closure-search
- --min-closure-exon $singlePaired.pParams.closure_search.min_closure_exon
- --min-closure-intron $singlePaired.pParams.closure_search.min_closure_intron
- --max-closure-intron $singlePaired.pParams.closure_search.max_closure_intron
- #else:
- --no-closure-search
- #end if
#if $singlePaired.pParams.coverage_search.use_search == "Yes":
--coverage-search
--min-coverage-intron $singlePaired.pParams.coverage_search.min_coverage_intron
@@ -206,7 +188,6 @@
<param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /><param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
- <param name="initial_read_mismatches" type="integer" min="0" value="2" label="Number of mismatches allowed in the initial read mapping" /><param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /><param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
@@ -245,19 +226,6 @@
<when value="No" /></conditional><!-- /own_junctions -->
- <!-- Closure search. -->
- <conditional name="closure_search">
- <param name="use_search" type="select" label="Use Closure Search">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
- </param>
- <when value="Yes">
- <param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." />
- <param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" />
- <param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" />
- </when>
- <when value="No" />
- </conditional><!-- Coverage search. --><conditional name="coverage_search"><param name="use_search" type="select" label="Use Coverage Search">
@@ -312,7 +280,6 @@
<param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /><param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
- <param name="initial_read_mismatches" type="integer" min="0" value="2" label="Number of mismatches allowed in the initial read mapping" /><param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /><param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /><!-- Options for supplying own junctions. -->
@@ -350,19 +317,6 @@
<when value="No" /></conditional><!-- /own_junctions -->
- <!-- Closure search. -->
- <conditional name="closure_search">
- <param name="use_search" type="select" label="Use Closure Search">
- <option value="No">No</option>
- <option value="Yes">Yes</option>
- </param>
- <when value="Yes">
- <param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." />
- <param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" />
- <param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" />
- </when>
- <when value="No" />
- </conditional><!-- Coverage search. --><conditional name="coverage_search"><param name="use_search" type="select" label="Use Coverage Search">
@@ -500,7 +454,7 @@
<test><!-- Tophat commands:
bowtie-build -f test-data/tophat_in1.fasta tophat_in1
- tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger
+ tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger
Replace the + with double-dash
Rename the files in tmp_dir appropriately
-->
@@ -527,10 +481,6 @@
<param name="use_juncs" value="No" /><param name="no_novel_juncs" value="No" /><param name="use_search" value="Yes" />
- <param name="min_closure_exon" value="50" />
- <param name="min_closure_intron" value="50" />
- <param name="max_closure_intron" value="5000" />
- <param name="use_search" value="Yes" /><param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /><param name="microexon_search" value="Yes" />
@@ -643,17 +593,11 @@
-G/--GTF [GTF 2.2 file] Supply TopHat with a list of gene model annotations. TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping.
-j/--raw-juncs [juncs file] Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-], left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive.
-no-novel-juncs Only look for junctions indicated in the supplied GFF file. (ignored without -G)
- --no-closure-search Disables the mate pair closure-based search for junctions. Currently, has no effect - closure search is off by default.
- --closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (about or less than 50bp)
--no-coverage-search Disables the coverage based search for junctions.
--coverage-search Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.
--microexon-search With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.
- --butterfly-search TopHat will use a slower but potentially more sensitive algorithm to find junctions in addition to its standard search. Consider using this if you expect that your experiment produced a lot of reads from pre-mRNA, that fall within the introns of your transcripts.
--segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2.
--segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25.
- --min-closure-exon During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50.
- --min-closure-intron The minimum intron length that may be found during closure search. The default is 50.
- --max-closure-intron The maximum intron length that may be found during closure search. The default is 5000.
--min-coverage-intron The minimum intron length that may be found during coverage search. The default is 50.
--max-coverage-intron The maximum intron length that may be found during coverage search. The default is 20000.
--min-segment-intron The minimum intron length that may be found during split-segment search. The default is 50.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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