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comparison chira_merge.xml @ 4:0170de5072d4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
author iuc
date Fri, 20 Mar 2020 05:11:17 -0400
parents ce26b5a859ba
children 35f433d0bd7f
comparison
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3:c96f1a93beb7 4:0170de5072d4
7 <command><![CDATA[ 7 <command><![CDATA[
8 chira_merge.py 8 chira_merge.py
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 -ao '$alignment_overlap'
14 -so '$segment_overlap' 13 -so '$segment_overlap'
14 #if str($merge.mode) == "blockbuster":
15 -bb
16 -d '$merge.distance'
17 -mc '$merge.min_cluster_height'
18 -mb '$merge.min_block_height'
19 -sc '$merge.scale'
20 #else:
21 -ao '$merge.alignment_overlap'
22 #end if
15 -o ./ 23 -o ./
16 ]]></command> 24 ]]></command>
17 25
18 <inputs> 26 <inputs>
19 <param format="bed" name="alignments" type="data" label="Input BED file of alignments"/> 27 <param format="bed" name="alignments" type="data" label="Input BED file of alignments"/>
25 <when value="yes"> 33 <when value="yes">
26 <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/> 34 <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/>
27 </when> 35 </when>
28 <when value="no"> 36 <when value="no">
29 <!-- Do nothing --> 37 <!-- Do nothing -->
30 </when> 38 </when>
31 </conditional> 39 </conditional>
32 <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1"
33 help="Minimum fraction of BED entries that must overlap inorder to merge"/>
34 <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1" 40 <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1"
35 help="Matching read positions with greater than this fraction overlap are merged into a segment"/> 41 help="Matching read positions with greater than this fraction overlap are merged into a segment"/>
42 <conditional name="merge">
43 <param name="mode" type="select" label="Select the mode of merging">
44 <option value="overlap">Overlap based</option>
45 <option value="blockbuster">Gaussian based (blockbuster)</option>
46 </param>
47 <when value="overlap">
48 <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1"
49 help="Minimum fraction of BED entries that must overlap inorder to merge"/>
50 </when>
51 <when value="blockbuster">
52 <param name="distance" type="integer" value="30" label="Blockbuster parameter distance"
53 help="Minimum distance between two clusters"/>
54 <param name="min_cluster_height" type="float" value="10" label="Blockbuster parameter minClusterHeight"
55 help="minimum height (readno) of a cluster"/>
56 <param name="min_block_height" type="float" value="1" label="Blockbuster parameter minBlockHeight"
57 help="minimum height (readno) of a block"/>
58 <param name="scale" type="float" value="0.4" label="Blockbuster parameter scale" min="0" max="1"
59 help="scale stddev for a single read"/>
60 </when>
61 </conditional>
36 </inputs> 62 </inputs>
37 <outputs> 63 <outputs>
38 <data format="bed" name="segments_bed" from_work_dir="segments.bed" label="ChiRA aligned read segments on ${on_string}"/> 64 <data format="bed" name="segments_bed" from_work_dir="segments.bed" label="ChiRA aligned read segments on ${on_string}"/>
39 <data format="tabular" name="merged_bed" from_work_dir="merged.bed" label="ChiRA merged alignments on ${on_string}"/> 65 <data format="tabular" name="merged_bed" from_work_dir="merged.bed" label="ChiRA merged alignments on ${on_string}"/>
40 </outputs> 66 </outputs>
41 67
42 <tests> 68 <tests>
43 <!-- Test: Map without annotation --> 69 <!-- Test: Merge without annotation -->
44 <test expect_num_outputs="2"> 70 <test expect_num_outputs="2">
45 <param name="alignments" value="alignments.bed"/> 71 <param name="alignments" value="alignments.bed"/>
46 <param name="choice" value="no" /> 72 <param name="choice" value="no" />
47 <output name="segments_bed" > 73 <output name="segments_bed" >
48 <assert_contents> 74 <assert_contents>
49 <has_text_matching expression="ENSMUST00000160533\t69\t82\t6|1|4,ENSMUST00000160533,69,82,+,42S13M\t0\t+" /> 75 <has_text_matching expression="ENSMUST00000160533\t69\t82\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t\+" />
50 </assert_contents> 76 </assert_contents>
51 </output> 77 </output>
52 <output name="merged_bed" > 78 <output name="merged_bed" >
53 <assert_contents> 79 <assert_contents>
54 <has_text_matching expression="ENSMUST00000182010\t19\t74\t+\t6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M" /> 80 <has_text_matching expression="ENSMUST00000182010\t408\t477\t\+" />
81 <has_text_matching expression="mmu-miR-106a-3p\t4\t15\t\+" />
55 </assert_contents> 82 </assert_contents>
56 </output> 83 </output>
57 </test> 84 </test>
58 <!-- Test: Map with annotation --> 85 <!-- Test: Merge with annotation -->
59 <test expect_num_outputs="2"> 86 <test expect_num_outputs="2">
60 <param name="alignments" value="alignments.bed" /> 87 <param name="alignments" value="alignments.bed" />
61 <param name="choice" value="yes" /> 88 <param name="choice" value="yes" />
62 <param name="gtf" value="annotation.gtf" /> 89 <param name="gtf" value="annotation.gtf" />
63 <output name="segments_bed" > 90 <output name="segments_bed" >
64 <assert_contents> 91 <assert_contents>
65 <has_text_matching expression="5\t137142331\t137142344\t6|1|4,ENSMUST00000160533,69,82,+,42S13M\t0\t-" /> 92 <has_text_matching expression="5\t137142331\t137142344\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t-" />
66 </assert_contents> 93 </assert_contents>
67 </output> 94 </output>
68 <output name="merged_bed" > 95 <output name="merged_bed" >
69 <assert_contents> 96 <assert_contents>
70 <has_text_matching expression="17\t39846976\t39847031\t+\t6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M" /> 97 <has_text_matching expression="17\t39846957\t39847016\t\+" />
98 <has_text_matching expression="5\t137142331\t137142344\t-" />
99 </assert_contents>
100 </output>
101 </test>
102 <!-- Test: Merge using blockbuster -->
103 <test expect_num_outputs="2">
104 <param name="alignments" value="alignments.bed" />
105 <param name="choice" value="yes" />
106 <param name="gtf" value="annotation.gtf" />
107 <param name="mode" value="blockbuster" />
108 <param name="min_cluster_height" value="5" />
109 <output name="segments_bed" >
110 <assert_contents>
111 <has_text_matching expression="5\t137142331\t137142344\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t-" />
112 </assert_contents>
113 </output>
114 <output name="merged_bed" >
115 <assert_contents>
116 <has_text_matching expression="17\t39846957\t39847016\t\+" />
71 </assert_contents> 117 </assert_contents>
72 </output> 118 </output>
73 </test> 119 </test>
74 </tests> 120 </tests>
75 121