Mercurial > repos > bgruening > hicexplorer_hiccomparematrices

comparison macros.xml @ 15:4f9305d3bb34 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
author iuc
date Tue, 05 Nov 2024 00:00:39 +0000
parents e03780179ee5
children
comparison
equal deleted inserted replaced
14:e03780179ee5 15:4f9305d3bb34
1 <macros> 1 <macros>
2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> 2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
3 <token name="@TOOL_VERSION@">3.7.5</token> 3 <token name="@TOOL_VERSION@">3.7.5</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">1</token>
5 <token name="@PROFILE@">23.0</token> 5 <token name="@PROFILE@">23.0</token>
6 <token name="@USE_RANGE@"> 6 <token name="@USE_RANGE@">
7 #if $use_range.select_use_range == "yes_use_range": 7 #if $use_range.select_use_range == "yes_use_range":
8 --range $use_range.range_min:$use_range.range_max 8 --range $use_range.range_min:$use_range.range_max
9 #end if 9 #end if
46 <xml name="dpi"> 46 <xml name="dpi">
47 <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' /> 47 <param argument='--dpi' type='integer' optional='true' min="10" max="1000" label='DPI for image' help='Change the default resolution of the plot.' />
48 </xml> 48 </xml>
49 49
50 <xml name="restrictionCutFile"> 50 <xml name="restrictionCutFile">
51 <param argument="--restrictionCutFile" type="data" format="bed" optional="false" 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 51 <param argument="--restrictionCutFile" type="data" format="bed" optional="false" 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
52 (i.e. the region between one restriction site and the next)." /> 52 (i.e. the region between one restriction site and the next)." />
53 </xml> 53 </xml>
54 54
55 <xml name="restrictionSequence"> 55 <xml name="restrictionSequence">
56 <param argument="--restrictionSequence" type="text" optional="false" 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 56 <param argument="--restrictionSequence" type="text" optional="false" 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
57 &quot;dangling-ends&quot;. If not given, such statistics will not be available."> 57 &quot;dangling-ends&quot;. If not given, such statistics will not be available.">
58 <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator> 58 <validator type="regex" message="Only space separated nucleotide sequences are allowed.">^(?:[ATCGatcg]+(?:\s[ATCGatcg]+)*)?$</validator>
59 </param> 59 </param>
60 </xml> 60 </xml>
61 <xml name="danglingSequence"> 61 <xml name="danglingSequence">
62 <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting. 62 <param argument="--danglingSequence" type="text" optional="false" label="Dangling sequence" help="Sequence left by the restriction enzyme after cutting.
63 Each restriction enzyme recognizes a different DNA sequence and, 63 Each restriction enzyme recognizes a different DNA sequence and,
65 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT. 65 For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
66 For DpnII, the restriction site and dangling end sequence are the same: GATC. 66 For DpnII, the restriction site and dangling end sequence are the same: GATC.
67 This information is easily found on the description of the restriction enzyme. 67 This information is easily found on the description of the restriction enzyme.
68 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads. 68 The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
69 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "> 69 A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. ">
70 <validator type="expression" message="Only alphabetic characters (a-z) are allowed.">value.isalpha()</validator> 70 <validator type="regex" message="Only space separated nucleotide sequences are allowed.">^(?:[ATCGatcg]+(?:\s[ATCGatcg]+)*)?$</validator>
71 </param> 71 </param>
72 </xml> 72 </xml>
73 73
74 <xml name="zMax"> 74 <xml name="zMax">
75 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" /> 75 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot" />