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comparison coverageBed.xml @ 45:b176b1c7949e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 69394918e7a50dad3ae578e932cbac27b96e0d3b
author iuc
date Tue, 24 Jul 2018 11:49:34 -0400
parents 71d71721695e
children 2f457890d8c8
comparison
equal deleted inserted replaced
44:9224d51be786 45:b176b1c7949e
1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.2"> 1 <tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.3">
2 <description>of features in file B on the features in file A (bedtools coverage)</description> 2 <description>of features in file B on the features in file A (bedtools coverage)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
24 $a_or_b 24 $a_or_b
25 -a '$inputA' 25 -a '$inputA'
26 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate': 26 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
27 -b '$reduce_or_iterate.inputB' 27 -b '$reduce_or_iterate.inputB'
28 #if $reduce_or_iterate.inputB.is_of_type('bam'): 28 #if $reduce_or_iterate.inputB.is_of_type('bam'):
29 -sorted -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5) 29 -sorted -g <(samtools view -H $reduce_or_iterate.inputB | grep '^@SQ' | sed $'s/\tSN:/\tSN\t/' | sed $'s/\tLN:/\tLN\t/' | cut -f 3,5)
30 #end if 30 #end if
31 #else: 31 #else:
32 #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB]) 32 #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
33 -b '$inputBs' 33 -b '$inputBs'
34 #end if 34 #end if
94 <param name="inputA" value="coverageBedA.bed" ftype="bed" /> 94 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
95 <param name="inputB" value="coverageBedB.bed" ftype="bed" /> 95 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
96 <output name="output" file="coverageBed_result1.bed" ftype="bed" /> 96 <output name="output" file="coverageBed_result1.bed" ftype="bed" />
97 </test> 97 </test>
98 <test> 98 <test>
99 <param name="inputA" value="multiCov1.bed" ftype="bed" />
100 <param name="inputB" value="srma_in3.bam" ftype="bam" />
101 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
102 </test>
103 <test>
104 <param name="inputA" value="multiCov1.bed" ftype="bed" />
105 <param name="reduce_or_iterate_selector" value="reduce" />
106 <param name="inputB" value="srma_in3.bam" ftype="bam" />
107 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
108 </test>
109 <test>
99 <param name="inputA" value="coverageBedA.bed" ftype="bed" /> 110 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
100 <param name="inputB" value="coverageBedB.bed" ftype="bed" /> 111 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
101 <param name="overlap_b" value="1" /> 112 <param name="overlap_b" value="1" />
102 <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" /> 113 <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" />
103 </test> 114 </test>