Mercurial > repos > iuc > chira_merge

comparison chira_merge.xml @ 8:c836a05bd6a3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
author iuc
date Fri, 29 May 2020 06:58:21 -0400
parents 35f433d0bd7f
children 948f4bc1f030
comparison
equal deleted inserted replaced
7:35f433d0bd7f 8:c836a05bd6a3
9 -b '$alignments' 9 -b '$alignments'
10 #if str($annotation.choice) == "yes": 10 #if str($annotation.choice) == "yes":
11 -g '$annotation.gtf' 11 -g '$annotation.gtf'
12 #end if 12 #end if
13 -so '$segment_overlap' 13 -so '$segment_overlap'
14 -lt '$length_threshold'
14 #if str($merge.mode) == "blockbuster": 15 #if str($merge.mode) == "blockbuster":
15 -bb 16 -bb
16 -d '$merge.distance' 17 -d '$merge.distance'
17 -mc '$merge.min_cluster_height' 18 -mc '$merge.min_cluster_height'
18 -mb '$merge.min_block_height' 19 -mb '$merge.min_block_height'
19 -sc '$merge.scale' 20 -sc '$merge.scale'
20 #else: 21 #else:
21 -ao '$merge.alignment_overlap' 22 -ao '$merge.alignment_overlap'
23 -ls '$merge.min_locus_size'
22 #end if 24 #end if
23 #if str($reference.ref_type) == "split": 25 #if str($reference.ref_type) == "split":
24 -f1 '$reference.ref_fasta1' 26 -f1 '$reference.ref_fasta1'
25 -f2 '$reference.ref_fasta2' 27 -f2 '$reference.ref_fasta2'
26 #end if 28 #end if
42 <!-- Do nothing --> 44 <!-- Do nothing -->
43 </when> 45 </when>
44 </conditional> 46 </conditional>
45 <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1" 47 <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1"
46 help="Matching read positions with greater than this fraction overlap are merged into a segment"/> 48 help="Matching read positions with greater than this fraction overlap are merged into a segment"/>
49 <param name="length_threshold" type="float" value="0.9" label="Minimum length of the alignments as a fraction of longest" min="0" max="1"
50 help="Consider the alignments of a that read have at least longer than this value times the longest alignment for that read"/>
47 <conditional name="merge"> 51 <conditional name="merge">
48 <param name="mode" type="select" label="Select the mode of merging"> 52 <param name="mode" type="select" label="Select the mode of merging">
49 <option value="overlap">Overlap based</option> 53 <option value="overlap">Overlap based</option>
50 <option value="blockbuster">Gaussian based (blockbuster)</option> 54 <option value="blockbuster">Gaussian based (blockbuster)</option>
51 </param> 55 </param>
52 <when value="overlap"> 56 <when value="overlap">
53 <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1" 57 <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1"
54 help="Minimum fraction of BED entries that must overlap inorder to merge"/> 58 help="Minimum fraction of BED entries that must overlap inorder to merge"/>
59 <param name="min_locus_size" type="integer" value="1" label="Minimum locus size"
60 help="Minimum number of alignments to be present to output the merged a locus"/>
55 </when> 61 </when>
56 <when value="blockbuster"> 62 <when value="blockbuster">
57 <param name="distance" type="integer" value="30" label="Blockbuster parameter distance" 63 <param name="distance" type="integer" value="30" label="Blockbuster parameter distance"
58 help="Minimum distance between two clusters"/> 64 help="Minimum distance between two clusters"/>
59 <param name="min_cluster_height" type="float" value="10" label="Blockbuster parameter minClusterHeight" 65 <param name="min_cluster_height" type="integer" value="10" label="Blockbuster parameter minClusterHeight"
60 help="minimum height (readno) of a cluster"/> 66 help="minimum height (readno) of a cluster"/>
61 <param name="min_block_height" type="float" value="1" label="Blockbuster parameter minBlockHeight" 67 <param name="min_block_height" type="integer" value="10" label="Blockbuster parameter minBlockHeight"
62 help="minimum height (readno) of a block"/> 68 help="minimum height (readno) of a block"/>
63 <param name="scale" type="float" value="0.4" label="Blockbuster parameter scale" min="0" max="1" 69 <param name="scale" type="float" value="0.1" label="Blockbuster parameter scale" min="0" max="1"
64 help="scale stddev for a single read"/> 70 help="scale stddev for a single read"/>
65 </when> 71 </when>
66 </conditional> 72 </conditional>
67 <conditional name="reference"> 73 <conditional name="reference">
68 <param name="ref_type" type="select" label="Did you use single or split reference for alignment?"> 74 <param name="ref_type" type="select" label="Did you use single or split reference for alignment?">
94 <param name="ref_type" value="split"/> 100 <param name="ref_type" value="split"/>
95 <param name="ref_fasta1" value="ref1.fasta"/> 101 <param name="ref_fasta1" value="ref1.fasta"/>
96 <param name="ref_fasta2" value="ref2.fasta"/> 102 <param name="ref_fasta2" value="ref2.fasta"/>
97 <output name="segments_bed" > 103 <output name="segments_bed" >
98 <assert_contents> 104 <assert_contents>
99 <has_text_matching expression="ENSMUST00000146006\t6703\t6718\t10\|2\|3,ENSMUST00000146006,6703,6718,\+,24S15M16S\t1\t\+" /> 105 <has_text_matching expression="ENSMUST00000037472\t672\t687\t2\|1\|4,ENSMUST00000037472,672,687,\+,14S15M25S\t1\t\+" />
100 </assert_contents> 106 </assert_contents>
101 </output> 107 </output>
102 <output name="merged_bed" > 108 <output name="merged_bed" >
103 <assert_contents> 109 <assert_contents>
104 <has_text_matching expression="ENSMUST00000182010\t408\t477\t\+" /> 110 <has_text_matching expression="ENSMUST00000182010\t408\t477\t\+" />
131 <test expect_num_outputs="2"> 137 <test expect_num_outputs="2">
132 <param name="alignments" value="alignments.bed" /> 138 <param name="alignments" value="alignments.bed" />
133 <param name="choice" value="yes" /> 139 <param name="choice" value="yes" />
134 <param name="gtf" value="annotation.gtf" /> 140 <param name="gtf" value="annotation.gtf" />
135 <param name="mode" value="blockbuster" /> 141 <param name="mode" value="blockbuster" />
142 <param name="min_block_height" value="1" />
136 <param name="min_cluster_height" value="5" /> 143 <param name="min_cluster_height" value="5" />
137 <param name="ref_type" value="split"/> 144 <param name="ref_type" value="split"/>
138 <param name="ref_fasta1" value="ref1.fasta"/> 145 <param name="ref_fasta1" value="ref1.fasta"/>
139 <param name="ref_fasta2" value="ref2.fasta"/> 146 <param name="ref_fasta2" value="ref2.fasta"/>
140 <output name="segments_bed" > 147 <output name="segments_bed" >