Mercurial > repos > bgruening > hicexplorer_hiccorrelate
comparison macros.xml @ 22:cd40ca76865a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 79133bc3739fbcc6c2055d589679aae312161d03
author | iuc |
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date | Tue, 05 Nov 2024 00:09:20 +0000 |
parents | 2786a931cad2 |
children | 0f5786ffa10d |
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21:2786a931cad2 | 22:cd40ca76865a |
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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 "dangling-ends". If not given, such statistics will not be available."> | 57 "dangling-ends". 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" /> |