Mercurial > repos > bgruening > hicexplorer_hicquickqc
diff hicQuickQC.xml @ 1:b599d3000966 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
| author | bgruening |
|---|---|
| date | Wed, 05 Feb 2020 19:53:34 -0500 |
| parents | 269c4246279d |
| children | 909125ec301f |
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--- a/hicQuickQC.xml Mon Dec 16 15:38:29 2019 -0500 +++ b/hicQuickQC.xml Wed Feb 05 19:53:34 2020 -0500 @@ -16,20 +16,6 @@ '${repeat.samFile}' #end for - #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile": - --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile' - --minDistance $restrictionCutFileBinSize_conditional.minDistance - --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize - #end if - - #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize": - --binSize - #for $repeat in $restrictionCutFileBinSize_conditional.binSizes - '${repeat.binSize}' - #end for - #end if - - #if $restrictionSequence: --restrictionSequence '$restrictionSequence' #end if @@ -50,33 +36,7 @@ help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file."> <param name="samFile" type="data" format="sam,qname_input_sorted.bam"/> </repeat> - <conditional name="restrictionCutFileBinSize_conditional"> - <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size"> - <option value="optionRestrictionCutFile">Restriction cut file</option> - <option value="optionBinSize" selected="True">Bin size</option> - </param> - <when value="optionRestrictionCutFile"> - <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)." /> - <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."/> - <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"> - <repeat name='binSizes' title='Bin size in bp' min="1" 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. Use multiple ones to create a mcool file."> - <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"/> - </repeat> - </when> - </conditional> - + <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." />