Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison hicBuildMatrix.xml @ 3:2a13bfe5bff2 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 1beb50fdb3f5f8fd60e3b9c3d44964d70075616d
author iuc
date Mon, 27 Nov 2017 11:15:32 -0500
parents eb0d14cdf8b8
children 652fdcbff650
comparison
equal deleted inserted replaced
2:eb0d14cdf8b8 3:2a13bfe5bff2
19 #end for 19 #end for
20 20
21 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile": 21 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile":
22 --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile' 22 --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile'
23 --minDistance $restrictionCutFileBinSize_conditional.minDistance 23 --minDistance $restrictionCutFileBinSize_conditional.minDistance
24 --maxDistance $restrictionCutFileBinSize_conditional.maxDistance 24 --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize
25 #end if 25 #end if
26 26
27 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize": 27 #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
28 --binSize $restrictionCutFileBinSize_conditional.binSize 28 --binSize $restrictionCutFileBinSize_conditional.binSize
29 #end if 29 #end if
69 <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size"> 69 <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size">
70 <option value="optionRestrictionCutFile">Restriction cut file</option> 70 <option value="optionRestrictionCutFile">Restriction cut file</option>
71 <option value="optionBinSize" selected="True">Bin size</option> 71 <option value="optionBinSize" selected="True">Bin size</option>
72 </param> 72 </param>
73 <when value="optionRestrictionCutFile"> 73 <when value="optionRestrictionCutFile">
74 <param argument="--restrictionCutFile" type="data" format="bed" optional="True" 74 <param argument="--restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
75 help="BED file with all restriction cut places. Should contain only mappable restriction sites. If given, the
76 bins are set to match the restriction fragments (i.e. the region between one restriction site and the next)"/>
77 <param name="restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
78 help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments 75 help="Should contaion only mappable restriction sites. If given, the bins are set to match the restriction fragments
79 (i.e. the region between one restriction site and the next)." argument="--restrictionCutFile"/> 76 (i.e. the region between one restriction site and the next)." />
80 <param name="minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites" 77 <param argument="--minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites"
81 help="Restriction sites that are closer that this distance are merged into one. 78 help="Restriction sites that are closer that this distance are merged into one.
82 This option only applies if --restrictionCutFile is given." argument="--minDistance"/> 79 This option only applies if --restrictionCutFile is given."/>
83 80 <param argument="--maxLibraryInsertSize" type="integer" value="" optional="true"
84 <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" 81 label="Maximum library insert size defines different cut offs based on the maximum expected library size"
85 help="This option only applies if --restrictionCutFile is given." argument="--maxDistance"/> 82 help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer)
83 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
84 belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate
85 is too far away from the nearest restriction site." />
86 </when> 86 </when>
87 <when value="optionBinSize"> 87 <when value="optionBinSize">
88 <param name="binSize" type="integer" value="" optional="true" label="Bin size in bp" 88 <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"
89 help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites. 89 help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
90 Otherwise all reads in the interval are considered. " argument="--binSize"/> 90 Otherwise all reads in the interval are considered. "/>
91 </when> 91 </when>
92 </conditional> 92 </conditional>
93 93
94 <param name="restrictionSequence" type="text" optional="true" label="Sequence of the restriction site" 94 <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
95 help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or 95 help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
96 &quot;dangling-ends&quot;. If not given, such statistics will not be available." argument="--restrictionSequence"/> 96 &quot;dangling-ends&quot;. If not given, such statistics will not be available." />
97 97
98 <expand macro="region" /> 98 <expand macro="region" />
99 99
100 <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue="" 100 <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue=""
101 label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. ' 101 label="Keep self circles"
102 + 'They will be counted and shown in the QC plots." /> 102 help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." />
103 103
104 <expand macro="minMappingQuality" /> 104 <expand macro="minMappingQuality" />
105 105
106 <param name="danglingSequence" type="text" optional="true" label="The dangling sequence" 106 <param argument="--danglingSequence" type="text" optional="true" label="The dangling sequence"
107 help="Dangling end sequence left by the restriction enzyme. For DpnII for example, 107 help="Dangling end sequence left by the restriction enzyme. For DpnII for example,
108 the dangling end is the same restriction sequence. This is used 108 the dangling end is the same restriction sequence. This is used
109 to discard reads that end/start with such sequence 109 to discard reads that end/start with such sequence
110 and that are considered un-ligated fragments or 110 and that are considered un-ligated fragments or
111 'dangling-ends'. If not given, such statistics will 111 'dangling-ends'. If not given, such statistics will
112 not be available." argument="--danglingSequence"/> 112 not be available."/>
113 </inputs> 113 </inputs>
114 <outputs> 114 <outputs>
115 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/> 115 <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
116 <data name="outFileName" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/> 116 <data name="outFileName" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/>
117 <data name="qc" format="html" label="${tool.name} QC"/> 117 <data name="qc" format="html" label="${tool.name} QC"/>