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comparison chira_merge.xml @ 7:35f433d0bd7f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
author iuc
date Thu, 07 May 2020 03:35:27 -0400
parents 0170de5072d4
children c836a05bd6a3
comparison
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6:7f9cf152cf8f 7:35f433d0bd7f
18 -mb '$merge.min_block_height' 18 -mb '$merge.min_block_height'
19 -sc '$merge.scale' 19 -sc '$merge.scale'
20 #else: 20 #else:
21 -ao '$merge.alignment_overlap' 21 -ao '$merge.alignment_overlap'
22 #end if 22 #end if
23 #if str($reference.ref_type) == "split":
24 -f1 '$reference.ref_fasta1'
25 -f2 '$reference.ref_fasta2'
26 #end if
27 $chimeric_only
23 -o ./ 28 -o ./
24 ]]></command> 29 ]]></command>
25 30
26 <inputs> 31 <inputs>
27 <param format="bed" name="alignments" type="data" label="Input BED file of alignments"/> 32 <param format="bed" name="alignments" type="data" label="Input BED file of alignments"/>
57 help="minimum height (readno) of a block"/> 62 help="minimum height (readno) of a block"/>
58 <param name="scale" type="float" value="0.4" label="Blockbuster parameter scale" min="0" max="1" 63 <param name="scale" type="float" value="0.4" label="Blockbuster parameter scale" min="0" max="1"
59 help="scale stddev for a single read"/> 64 help="scale stddev for a single read"/>
60 </when> 65 </when>
61 </conditional> 66 </conditional>
67 <conditional name="reference">
68 <param name="ref_type" type="select" label="Did you use single or split reference for alignment?">
69 <option value="single">Single reference</option>
70 <option value="split">Split reference</option>
71 </param>
72 <when value="split">
73 <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file"
74 help="Reference fasta file"/>
75 <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file"
76 help="Second reference fasta file."/>
77 </when>
78 <when value="single">
79 <!-- no need to provide a fasta file -->
80 </when>
81 </conditional>
82 <param name="chimeric_only" type="boolean" truevalue="-c" falsevalue="" checked="false" />
62 </inputs> 83 </inputs>
63 <outputs> 84 <outputs>
64 <data format="bed" name="segments_bed" from_work_dir="segments.bed" label="ChiRA aligned read segments on ${on_string}"/> 85 <data format="bed" name="segments_bed" from_work_dir="segments.bed" label="ChiRA aligned read segments on ${on_string}"/>
65 <data format="tabular" name="merged_bed" from_work_dir="merged.bed" label="ChiRA merged alignments on ${on_string}"/> 86 <data format="tabular" name="merged_bed" from_work_dir="merged.bed" label="ChiRA merged alignments on ${on_string}"/>
66 </outputs> 87 </outputs>
68 <tests> 89 <tests>
69 <!-- Test: Merge without annotation --> 90 <!-- Test: Merge without annotation -->
70 <test expect_num_outputs="2"> 91 <test expect_num_outputs="2">
71 <param name="alignments" value="alignments.bed"/> 92 <param name="alignments" value="alignments.bed"/>
72 <param name="choice" value="no" /> 93 <param name="choice" value="no" />
94 <param name="ref_type" value="split"/>
95 <param name="ref_fasta1" value="ref1.fasta"/>
96 <param name="ref_fasta2" value="ref2.fasta"/>
73 <output name="segments_bed" > 97 <output name="segments_bed" >
74 <assert_contents> 98 <assert_contents>
75 <has_text_matching expression="ENSMUST00000160533\t69\t82\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t\+" /> 99 <has_text_matching expression="ENSMUST00000146006\t6703\t6718\t10\|2\|3,ENSMUST00000146006,6703,6718,\+,24S15M16S\t1\t\+" />
76 </assert_contents> 100 </assert_contents>
77 </output> 101 </output>
78 <output name="merged_bed" > 102 <output name="merged_bed" >
79 <assert_contents> 103 <assert_contents>
80 <has_text_matching expression="ENSMUST00000182010\t408\t477\t\+" /> 104 <has_text_matching expression="ENSMUST00000182010\t408\t477\t\+" />
81 <has_text_matching expression="mmu-miR-106a-3p\t4\t15\t\+" /> 105 <has_text_matching expression="mmu-miR-9-5p\t0\t23\t\+" />
82 </assert_contents> 106 </assert_contents>
83 </output> 107 </output>
84 </test> 108 </test>
85 <!-- Test: Merge with annotation --> 109 <!-- Test: Merge with annotation -->
86 <test expect_num_outputs="2"> 110 <test expect_num_outputs="2">
87 <param name="alignments" value="alignments.bed" /> 111 <param name="alignments" value="alignments.bed" />
88 <param name="choice" value="yes" /> 112 <param name="choice" value="yes" />
89 <param name="gtf" value="annotation.gtf" /> 113 <param name="gtf" value="annotation.gtf" />
114 <param name="ref_type" value="split"/>
115 <param name="ref_fasta1" value="ref1.fasta"/>
116 <param name="ref_fasta2" value="ref2.fasta"/>
90 <output name="segments_bed" > 117 <output name="segments_bed" >
91 <assert_contents> 118 <assert_contents>
92 <has_text_matching expression="5\t137142331\t137142344\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t-" /> 119 <has_text_matching expression="2\t31033086\t31033109\t38\|2\|2,ENSMUST00000113555,1676,1699,\+,32S23M\t1\t-" />
120 <has_text_matching expression="7\t83738820\t83738843\t38\|2\|1,mmu-miR-9-5p,0,23,\+,5S23M27S\t1\t\+" />
93 </assert_contents> 121 </assert_contents>
94 </output> 122 </output>
95 <output name="merged_bed" > 123 <output name="merged_bed" >
96 <assert_contents> 124 <assert_contents>
97 <has_text_matching expression="17\t39846957\t39847016\t\+" /> 125 <has_text_matching expression="2\t31033086\t31033109\t-" />
98 <has_text_matching expression="5\t137142331\t137142344\t-" /> 126 <has_text_matching expression="7\t83738820\t83738843\t\+" />
99 </assert_contents> 127 </assert_contents>
100 </output> 128 </output>
101 </test> 129 </test>
102 <!-- Test: Merge using blockbuster --> 130 <!-- Test: Merge using blockbuster -->
103 <test expect_num_outputs="2"> 131 <test expect_num_outputs="2">
104 <param name="alignments" value="alignments.bed" /> 132 <param name="alignments" value="alignments.bed" />
105 <param name="choice" value="yes" /> 133 <param name="choice" value="yes" />
106 <param name="gtf" value="annotation.gtf" /> 134 <param name="gtf" value="annotation.gtf" />
107 <param name="mode" value="blockbuster" /> 135 <param name="mode" value="blockbuster" />
108 <param name="min_cluster_height" value="5" /> 136 <param name="min_cluster_height" value="5" />
137 <param name="ref_type" value="split"/>
138 <param name="ref_fasta1" value="ref1.fasta"/>
139 <param name="ref_fasta2" value="ref2.fasta"/>
109 <output name="segments_bed" > 140 <output name="segments_bed" >
110 <assert_contents> 141 <assert_contents>
111 <has_text_matching expression="5\t137142331\t137142344\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t-" /> 142 <has_text_matching expression="2\t31033086\t31033109\t38\|2\|2,ENSMUST00000113555,1676,1699,\+,32S23M\t1\t-" />
143 <has_text_matching expression="7\t83738820\t83738843\t38\|2\|1,mmu-miR-9-5p,0,23,\+,5S23M27S\t1\t\+" />
112 </assert_contents> 144 </assert_contents>
113 </output> 145 </output>
114 <output name="merged_bed" > 146 <output name="merged_bed" >
115 <assert_contents> 147 <assert_contents>
116 <has_text_matching expression="17\t39846957\t39847016\t\+" /> 148 <has_text_matching expression="7\t83738820\t83738843\t\+" />
149 </assert_contents>
150 </output>
151 </test>
152 <!-- Test: Chimeric only without annotation -->
153 <test expect_num_outputs="2">
154 <param name="alignments" value="alignments.bed"/>
155 <param name="choice" value="no" />
156 <param name="ref_type" value="split"/>
157 <param name="ref_fasta1" value="ref1.fasta"/>
158 <param name="ref_fasta2" value="ref2.fasta"/>
159 <param name="chimeric_only" value="true"/>
160 <output name="segments_bed" >
161 <assert_contents>
162 <has_text_matching expression="mmu-miR-9-5p\t0\t23\t38\|2\|1,mmu-miR-9-5p,0,23,\+,5S23M27S\t1\t\+" />
163 <has_text_matching expression="ENSMUST00000113555\t1676\t1699\t38\|2\|2,ENSMUST00000113555,1676,1699,\+,32S23M\t1\t\+" />
164 </assert_contents>
165 </output>
166 <output name="merged_bed" >
167 <assert_contents>
168 <has_text_matching expression="ENSMUST00000113555\t1676\t1699\t\+" />
169 <has_text_matching expression="mmu-miR-9-5p\t0\t23\t\+" />
117 </assert_contents> 170 </assert_contents>
118 </output> 171 </output>
119 </test> 172 </test>
120 </tests> 173 </tests>
121 174