# HG changeset patch
# User sauria
# Date 1433527740 14400
# Node ID 0a9c76d80e33216c2190902b81b181c165710316
planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
diff -r 000000000000 -r 0a9c76d80e33 hifive.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hifive.xml Fri Jun 05 14:09:00 2015 -0400
@@ -0,0 +1,390 @@
+
+
+ manipulate, analyze, and plot HiC and 5C chromatin interaction data
+
+ hifive_macros.xml
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+ (command["command_select"] == "hic-complete")
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+ (command["command_select"] == "hic-complete")
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+ (command["command_select"] == "hic-complete")
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+ (command["command_select"] == "fends")
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+ (command["command_select"] == "hic-data")
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+ (command["command_select"] == "hic-project")
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+ (command["command_select"] == "hic-normalize")
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+ (command["command_select"] == "hic-heatmap")
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+ (command["command_select"] == "hic-heatmap")
+ (command["image"]["generate"] == "yes")
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+ (command["command_select"] == "hic-interval")
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+ (command["command_select"] == "hic-interval")
+ (command["image"]["generate"] == "yes")
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+ (command["command_select"] == "5c-complete")
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+ (command["command_select"] == "5c-complete")
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+ (command["command_select"] == "5c-complete")
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+ (command["command_select"] == "fragments")
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+ (command["command_select"] == "5c-data")
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+ (command["command_select"] == "5c-project")
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+ (command["command_select"] == "5c-normalize")
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+ (command["command_select"] == "5c-heatmap")
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+ (command["command_select"] == "5c-heatmap")
+ (command["image"]["generate"] == "yes")
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+ (command["command_select"] == "5c-interval")
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+ (command["command_select"] == "5c-interval")
+ (command["image"]["generate"] == "yes")
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diff -r 000000000000 -r 0a9c76d80e33 hifive_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hifive_macros.xml Fri Jun 05 14:09:00 2015 -0400
@@ -0,0 +1,816 @@
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+ hifive
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+ 0.1
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+-B $command.bed
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+-i $command.insert
+#if str( $command.datafile.format ) == "bam":
+ #for $bam_file in $command.datafile.paired_bam:
+ --bam ${bam_file.readend1} ${bam_file.readend2}
+ #end for
+#elif str( $command.datafile.format ) == "mat":
+ --mat ${command.datafile.mat}
+#else:
+ #for raw_file in $command.datafile.raw_files:
+ --raw ${raw_file.raw}
+ #end for
+#end if
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+-f $command.minint
+-j $command.minbin
+-n $command.numbin
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+-m $command.filtermin
+-x $command.filtermax
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+#if str( $command.chroms ) != "":
+ -c $command.chroms
+#end if
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+$command.analysis.algorithm
+#if str( $command.analysis.algorithm ) == "probability" or str( $command.analysis.algorithm ) == "binning-probability":
+ -b $command.analysis.probiter
+ -l $command.analysis.step
+ -g $command.analysis.change
+ $command.analysis.precalc
+#end if
+#if str( $command.analysis.algorithm ) == "express" or str( $command.analysis.algorithm ) == "binning-express" :
+ $command.analysis.removedist
+ -w $command.analysis.expreads
+ $command.analysis.binary
+ -g $command.analysis.change
+ #if str( $command.analysis.subalgorithm.kr ) == "yes":
+ -z
+ #else
+ -e $command.analysis.expiter
+ #end if
+#end if
+#if str( $command.analysis.algorithm ) == "binning" or str( $command.analysis.algorithm ) == "binning-express" or str( $command.analysis.algorithm ) == "binning-probability":
+ -r $command.analysis.biniter
+ -t $command.analysis.threshold
+ -y $command.analysis.binreads
+ -v $command.analysis.model
+ -s $command.analysis.modelbins
+ -u $command.analysis.modeltypes
+ --pseudocounts $command.analysis.pseudo
+#end if
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+-d $command.datatype
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+$command.bed
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+#if str( $command.datafile.format ) == "bam":
+ #for $bam_file in $command.datafile.paired_bam:
+ -B ${bam_file.readend1} ${bam_file.readend2}
+ #end for
+#else:
+ #for $count_file in $command.datafile.count_files:
+ -C ${count_file.count}
+ #end for
+#end if
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+-f $command.minint
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+-m $command.mindist
+-x $command.maxdist
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+#if str( $command.regions ) != "":
+ -r $command.regions
+#end if
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+$command.analysis.algorithm
+#if str( $command.analysis.algorithm ) == "probability" or str( $command.analysis.algorithm ) == "binning-probability" or str( $command.analysis.algorithm ) == "probability-binning":
+ -b $command.analysis.probiter
+ -l $command.analysis.step
+ -g $command.analysis.change
+ $command.analysis.precalc
+#end if
+#if str( $command.analysis.algorithm ) == "express" or str( $command.analysis.algorithm ) == "binning-express" or str( $command.analysis.algorithm ) == "probability-express":
+ $command.analysis.removedist
+ -w $command.analysis.expreads
+ #if str( $command.analysis.subalgorithm.kr ) == "yes":
+ -z
+ #else:
+ -e $command.analysis.expiter
+ $command.analysis.logged
+ #end if
+#end if
+#if str( $command.analysis.algorithm ) == "binning" or str( $command.analysis.algorithm ) == "binning-express" or str( $command.analysis.algorithm ) == "binning-probability" or str( $command.analysis.algorithm ) == "express-binning" or str( $command.analysis.algorithm ) == "probability-binning":
+ -i $command.analysis.biniter
+ -t $command.analysis.threshold
+ -y $command.analysis.binreads
+ -v $command.analysis.model
+ -n $command.analysis.modelbins
+ -u $command.analysis.modeltypes
+#end if
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+-d $command.datatype
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+-b $command.binsize
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+#if str( $command.dynamic.binning ) == "yes":
+ -y
+ -x $command.dynamic.expbinsize
+ -f $command.dynamic.minobs
+ -a $command.dynamic.search
+ $command.dynamic.failed
+#end if
+
+
+#if str( $command.dynamic.binning ) == "yes":
+ -y
+ -x $command.dynamic.expbinsize
+ -f $command.dynamic.minobs
+ -g $command.dynamic.search
+ $command.dynamic.failed
+#end if
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+-k min_color=$command.image.mincolor
+-k mid_color=$command.image.midcolor
+-k max_color=$command.image.maxcolor
+-k logged=$command.image.logged
+#if $command.image.minscore:
+ -k minscore=$command.image.minscore
+#end if
+#if $command.image.maxscore:
+ -k maxscore=$command.image.maxscore
+#end if
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+$command.image.rotate
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diff -r 000000000000 -r 0a9c76d80e33 readme.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst Fri Jun 05 14:09:00 2015 -0400
@@ -0,0 +1,68 @@
+=============================
+Galaxy wrapper for HiFive
+=============================
+
+This wrapper allows use of the hifive package, a set of tools for handling HiC
+and 5C data, on Galaxy. This includes managing data from mapped reads, either
+in bam, mat, or raw formats. All stages use hdf5 dictionaries for fast access
+and minimal memory and storage usage.
+
+This toolset includes methods for normalizing data from either HiC or 5C
+experiments at the fragment-end, or fragment level resolution, respectively.
+Once normalized, data can be used for plotting, binning, or other statistical
+tests within the package very quickly.
+
+Original documentation can be found `here `_.
+
+Automated Installation
+======================
+
+Galaxy should be able to automatically install the dependencies, i.e. the
+``h5py`` and ``hifive`` tool depedency packages.
+
+Manual Installation
+===================
+
+For those not using Galaxy's automated installation from the Tool Shed, put
+the XML and Python files in the ``tools/hifive/`` folder and add the
+XML files to your ``tool_conf.xml`` as normal. For example, use::
+
+
+
+
+================
+Wrapper Licence
+================
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff -r 000000000000 -r 0a9c76d80e33 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Jun 05 14:09:00 2015 -0400
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