Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison hicBuildMatrix.xml @ 15:231687cac31b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 06:55:00 -0400
parents 4b85ea34afae
children 9edf8894a22d
comparison
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14:76b189fd277b 15:231687cac31b
23 --minDistance $restrictionCutFileBinSize_conditional.minDistance 23 --minDistance $restrictionCutFileBinSize_conditional.minDistance
24 --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize 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 28 --binSize
29 #for $repeat in $restrictionCutFileBinSize_conditional.binSizes 29 #for $repeat in $restrictionCutFileBinSize_conditional.binSizes
30 '${repeat.binSize}' 30 '${repeat.binSize}'
31 #end for 31 #end for
32 #end if 32 #end if
33 33
70 #end if 70 #end if
71 71
72 ]]> 72 ]]>
73 </command> 73 </command>
74 <inputs> 74 <inputs>
75 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" 75 <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)"
76 help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file."> 76 help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
77 <param name="samFile" type="data" format="sam,qname_input_sorted.bam"/> 77 <param name="samFile" type="data" format="sam,qname_input_sorted.bam"/>
78 </repeat> 78 </repeat>
79 <conditional name="restrictionCutFileBinSize_conditional"> 79 <conditional name="restrictionCutFileBinSize_conditional">
80 <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size"> 80 <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size">
115 115
116 <expand macro="minMappingQuality" /> 116 <expand macro="minMappingQuality" />
117 117
118 <param argument="--danglingSequence" type="text" optional="true" label="Dangling sequence" 118 <param argument="--danglingSequence" type="text" optional="true" label="Dangling sequence"
119 help="Sequence left by the restriction enzyme after cutting. 119 help="Sequence left by the restriction enzyme after cutting.
120 Each restriction enzyme recognizes a different DNA sequence and, 120 Each restriction enzyme recognizes a different DNA sequence and,
121 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence. 121 after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
122 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT. 122 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
123 For DpnII, the restriction site and dangling end sequence are the same: GATC. 123 For DpnII, the restriction site and dangling end sequence are the same: GATC.
124 This information is easily found on the description of the restriction enzyme. 124 This information is easily found on the description of the restriction enzyme.
125 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads. 125 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
126 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "/> 126 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "/>
127 127
128 <param name='outBam_Boolean' type='boolean' truevalue='--outBam' falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file" 128 <param name='outBam_Boolean' type='boolean' truevalue='--outBam' falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file"