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comparison coverageBed.xml @ 37:ce3c7f062223 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
author iuc
date Tue, 23 Mar 2021 20:23:14 +0000
parents b28e0cfa7ba1
children 3e38c9b3214f
comparison
equal deleted inserted replaced
36:0a5c785ac6db 37:ce3c7f062223
22 $reciprocal_overlap 22 $reciprocal_overlap
23 $a_or_b 23 $a_or_b
24 -a '$inputA' 24 -a '$inputA'
25 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate': 25 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
26 -b '$reduce_or_iterate.inputB' 26 -b '$reduce_or_iterate.inputB'
27 #if $reduce_or_iterate.inputB.is_of_type('bam'):
28 -sorted -g <(samtools view -H $reduce_or_iterate.inputB | grep '^@SQ' | sed $'s/\tSN:/\tSN\t/' | sed $'s/\tLN:/\tLN\t/' | cut -f 3,5)
29 #end if
30 #else: 27 #else:
31 -b 28 -b
32 #for $file in $reduce_or_iterate.inputB 29 #for $file in $reduce_or_iterate.inputB
33 '$file' 30 '$file'
34 #end for 31 #end for
35 #end if 32 #end if
33 @SORTED@
36 #if $inputA.is_of_type('gff'): 34 #if $inputA.is_of_type('gff'):
37 | sort -k1,1 -k4,2n 35 | sort -k1,1 -k4,2n
38 #else: 36 #else:
39 | sort -k1,1 -k2,2n 37 | sort -k1,1 -k2,2n
40 #end if 38 #end if
71 label="Require that the fraction overlap be reciprocal for A AND B." 69 label="Require that the fraction overlap be reciprocal for A AND B."
72 help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B" /> 70 help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B" />
73 <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" 71 <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
74 label="Require that the minimum fraction be satisfied for A OR B." 72 label="Require that the minimum fraction be satisfied for A OR B."
75 help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied" /> 73 help="If -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied" />
74 <!-- -sorted -g -->
75 <expand macro="sorted" />
76 </inputs> 76 </inputs>
77 <outputs> 77 <outputs>
78 <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/> 78 <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
79 </outputs> 79 </outputs>
80 <tests> 80 <tests>
84 <output name="output" file="coverageBed_result1.bed" ftype="bed" /> 84 <output name="output" file="coverageBed_result1.bed" ftype="bed" />
85 </test> 85 </test>
86 <test> 86 <test>
87 <param name="inputA" value="multiCov1.bed" ftype="bed" /> 87 <param name="inputA" value="multiCov1.bed" ftype="bed" />
88 <param name="inputB" value="srma_in3.bam" ftype="bam" /> 88 <param name="inputB" value="srma_in3.bam" ftype="bam" />
89 <param name="sorted" value="true"/>
89 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" /> 90 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
90 </test> 91 </test>
91 <test> 92 <test>
92 <param name="inputA" value="multiCov1.bed" ftype="bed" /> 93 <param name="inputA" value="multiCov1.bed" ftype="bed" />
93 <param name="reduce_or_iterate_selector" value="reduce" /> 94 <param name="reduce_or_iterate_selector" value="reduce" />
94 <param name="inputB" value="srma_in3.bam" ftype="bam" /> 95 <param name="inputB" value="srma_in3.bam" ftype="bam" />
96 <param name="sorted" value="true"/>
95 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" /> 97 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
96 </test> 98 </test>
97 <test> 99 <test>
98 <param name="inputA" value="coverageBedA.bed" ftype="bed" /> 100 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
99 <param name="inputB" value="coverageBedB.bed" ftype="bed" /> 101 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
104 <param name="inputA" value="coverageBedA.bed" ftype="bed" /> 106 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
105 <param name="inputB" value="coverageBedB.bed" ftype="bed" /> 107 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
106 <param name="overlap_a" value="1E-5" /> 108 <param name="overlap_a" value="1E-5" />
107 <param name="reciprocal_overlap" value="true" /> 109 <param name="reciprocal_overlap" value="true" />
108 <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" /> 110 <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />
111 </test>
112 <test>
113 <param name="inputA" value="multiCov1.bed" ftype="bed" />
114 <param name="reduce_or_iterate_selector" value="reduce" />
115 <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam" />
116 <param name="sorted" value="true"/>
117 <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed" />
118 </test>
119 <test>
120 <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
121 <param name="inputB" value="coverageBed.bam" ftype="bam" />
122 <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />
109 </test> 123 </test>
110 </tests> 124 </tests>
111 <help><![CDATA[ 125 <help><![CDATA[
112 **What it does** 126 **What it does**
113 127