Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix
changeset 4:1cf8c2444b44 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 1beb50fdb3f5f8fd60e3b9c3d44964d70075616d
| author | iuc |
|---|---|
| date | Mon, 27 Nov 2017 08:38:04 -0500 |
| parents | 41d4044e1dfe |
| children | 654282127b45 |
| files | hicBuildMatrix.xml macros.xml |
| diffstat | 2 files changed, 21 insertions(+), 21 deletions(-) [+] |
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--- a/hicBuildMatrix.xml Thu Nov 02 10:51:55 2017 -0400 +++ b/hicBuildMatrix.xml Mon Nov 27 08:38:04 2017 -0500 @@ -21,7 +21,7 @@ #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile": --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile' --minDistance $restrictionCutFileBinSize_conditional.minDistance - --maxDistance $restrictionCutFileBinSize_conditional.maxDistance + --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize #end if #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize": @@ -71,45 +71,45 @@ <option value="optionBinSize" selected="True">Bin size</option> </param> <when value="optionRestrictionCutFile"> - <param argument="--restrictionCutFile" type="data" format="bed" optional="True" - help="BED file with all restriction cut places. Should contain only mappable restriction sites. If given, the - bins are set to match the restriction fragments (i.e. the region between one restriction site and the next)"/> - <param name="restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places" + <param argument="--restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places" help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments - (i.e. the region between one restriction site and the next)." argument="--restrictionCutFile"/> - <param name="minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites" + (i.e. the region between one restriction site and the next)." /> + <param argument="--minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites" help="Restriction sites that are closer that this distance are merged into one. - This option only applies if --restrictionCutFile is given." argument="--minDistance"/> - - <param name="maxDistance" type="integer" value="" optional="true" label="Maximum distance in bp from restriction site to read, to consider a read a valid one" - help="This option only applies if --restrictionCutFile is given." argument="--maxDistance"/> + This option only applies if --restrictionCutFile is given."/> + <param argument="--maxLibraryInsertSize" type="integer" value="" optional="true" + label="Maximum library insert size defines different cut offs based on the maximum expected library size" + help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer) + which usually is between 800 to 1500 bp. If this value if not known use the default of 1000. The insert value is used to decide if two mates + belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate + is too far away from the nearest restriction site." /> </when> <when value="optionBinSize"> - <param name="binSize" type="integer" value="" optional="true" label="Bin size in bp" - help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites. - Otherwise all reads in the interval are considered. " argument="--binSize"/> + <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp" + help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites. + Otherwise all reads in the interval are considered. "/> </when> </conditional> - <param name="restrictionSequence" type="text" optional="true" label="Sequence of the restriction site" + <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site" help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or - "dangling-ends". If not given, such statistics will not be available." argument="--restrictionSequence"/> + "dangling-ends". If not given, such statistics will not be available." /> <expand macro="region" /> <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue="" - label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. ' - + 'They will be counted and shown in the QC plots." /> + label="Keep self circles" + help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." /> <expand macro="minMappingQuality" /> - <param name="danglingSequence" type="text" optional="true" label="The dangling sequence" + <param argument="--danglingSequence" type="text" optional="true" label="The dangling sequence" help="Dangling end sequence left by the restriction enzyme. For DpnII for example, the dangling end is the same restriction sequence. This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or 'dangling-ends'. If not given, such statistics will - not be available." argument="--danglingSequence"/> + not be available."/> </inputs> <outputs> <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
--- a/macros.xml Thu Nov 02 10:51:55 2017 -0400 +++ b/macros.xml Mon Nov 27 08:38:04 2017 -0500 @@ -1,6 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">1.8</token> + <token name="@WRAPPER_VERSION@">1.8.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>