Mercurial > repos > iuc > chira_merge
comparison chira_merge.xml @ 9:948f4bc1f030 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit a69b18084d0a9ade4e29869f8b0e2ce5fc4e0b73"
author | iuc |
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date | Sat, 06 Jun 2020 08:17:43 -0400 |
parents | c836a05bd6a3 |
children | 6492560fe1b4 |
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8:c836a05bd6a3 | 9:948f4bc1f030 |
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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 '$length_threshold' | 14 -lt '$length_threshold' |
15 -ao '$alignment_overlap' | |
15 #if str($merge.mode) == "blockbuster": | 16 #if str($merge.mode) == "blockbuster": |
16 -bb | 17 -bb |
17 -d '$merge.distance' | 18 -d '$merge.distance' |
18 -mc '$merge.min_cluster_height' | 19 -mc '$merge.min_cluster_height' |
19 -mb '$merge.min_block_height' | 20 -mb '$merge.min_block_height' |
20 -sc '$merge.scale' | 21 -sc '$merge.scale' |
21 #else: | 22 #else: |
22 -ao '$merge.alignment_overlap' | |
23 -ls '$merge.min_locus_size' | 23 -ls '$merge.min_locus_size' |
24 #end if | 24 #end if |
25 #if str($reference.ref_type) == "split": | 25 #if str($reference.ref_type) == "split": |
26 -f1 '$reference.ref_fasta1' | 26 -f1 '$reference.ref_fasta1' |
27 -f2 '$reference.ref_fasta2' | 27 -f2 '$reference.ref_fasta2' |
46 </conditional> | 46 </conditional> |
47 <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" |
48 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" | 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"/> | 50 help="Consider the alignments of a that read have at least longer than this value times the longest alignment for that read"/> |
51 <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments/blocks" min="0" max="1" | |
52 help="Minimum fraction of BED entries/blockbuster blocks that must overlap inorder to merge"/> | |
51 <conditional name="merge"> | 53 <conditional name="merge"> |
52 <param name="mode" type="select" label="Select the mode of merging"> | 54 <param name="mode" type="select" label="Select the mode of merging"> |
53 <option value="overlap">Overlap based</option> | 55 <option value="overlap">Overlap based</option> |
54 <option value="blockbuster">Gaussian based (blockbuster)</option> | 56 <option value="blockbuster">Gaussian based (blockbuster)</option> |
55 </param> | 57 </param> |
56 <when value="overlap"> | 58 <when value="overlap"> |
57 <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1" | |
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" | 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"/> | 60 help="Minimum number of alignments to be present to output the merged a locus"/> |
61 </when> | 61 </when> |
62 <when value="blockbuster"> | 62 <when value="blockbuster"> |
63 <param name="distance" type="integer" value="30" label="Blockbuster parameter distance" | 63 <param name="distance" type="integer" value="30" label="Blockbuster parameter distance" |
138 <param name="alignments" value="alignments.bed" /> | 138 <param name="alignments" value="alignments.bed" /> |
139 <param name="choice" value="yes" /> | 139 <param name="choice" value="yes" /> |
140 <param name="gtf" value="annotation.gtf" /> | 140 <param name="gtf" value="annotation.gtf" /> |
141 <param name="mode" value="blockbuster" /> | 141 <param name="mode" value="blockbuster" /> |
142 <param name="min_block_height" value="1" /> | 142 <param name="min_block_height" value="1" /> |
143 <param name="min_cluster_height" value="5" /> | 143 <param name="min_cluster_height" value="0" /> |
144 <param name="ref_type" value="split"/> | 144 <param name="ref_type" value="split"/> |
145 <param name="ref_fasta1" value="ref1.fasta"/> | 145 <param name="ref_fasta1" value="ref1.fasta"/> |
146 <param name="ref_fasta2" value="ref2.fasta"/> | 146 <param name="ref_fasta2" value="ref2.fasta"/> |
147 <output name="segments_bed" > | 147 <output name="segments_bed" > |
148 <assert_contents> | 148 <assert_contents> |