Mercurial > repos > iuc > ngsutils_bam_filter

comparison bam_filter.xml @ 3:9b9ae5963d3c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
author iuc
date Mon, 23 Oct 2017 13:27:02 -0400
parents 8187a729d9f4
children aecfe10118ed
comparison
equal deleted inserted replaced
2:7a68005de299 3:9b9ae5963d3c
1 <tool id="ngsutils_bam_filter" name="BAM filter" version="@WRAPPER_VERSION@.1"> 1 <tool id="ngsutils_bam_filter" name="BAM filter" version="@WRAPPER_VERSION@">
2 <description>Removes reads from a BAM file based on criteria</description> 2 <description>Removes reads from a BAM file based on criteria</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" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version" /> 8 <expand macro="version" />
9 <command><![CDATA[ 9 <command><![CDATA[
10 10 ## If the tool is executed with no filtering option,
11 ## If the tool is executed with no filtering option, 11 ## the default parameters simply copy over the input file
12 ## the default parameters simply copy over the input file 12 if grep -q "\w" '${parameters}'; then
13 if grep -q "\w" ${parameters}; 13 '$__tool_directory__/filter.py'
14 then 14 '$infile'
15 $__tool_directory__/filter.py 15 '$outfile'
16 $infile 16 `cat ${parameters}`;
17 $outfile 17 else
18 `cat ${parameters}`; 18 cp '$infile' '$outfile';
19 else 19 fi
20 cp $infile $outfile; 20 ]]></command>
21 fi
22
23 ]]>
24 </command>
25 <configfiles> 21 <configfiles>
26 <configfile name="parameters"> 22 <configfile name="parameters"><![CDATA[
27 <![CDATA[ 23 #if $minlen:
28 #if $minlen: 24 -minlen $minlen
29 -minlen $minlen 25 #end if
30 #end if 26 #if $maxlen
31 #if $maxlen 27 -maxlen $maxlen
32 -maxlen $maxlen 28 #end if
33 #end if 29 $mapped
34 $mapped 30 $unmapped
35 $unmapped 31 $properpair
36 $properpair 32 $noproperpair
37 $noproperpair 33 #if $mask:
38 #if $mask: 34 -mask ${mask}
39 -mask ${mask} 35 #end if
40 #end if 36 #if int($uniq) > -1:
41 #if int($uniq) > -1: 37 -uniq
42 -uniq 38 #if int($uniq) > 0:
43 #if int($uniq) > 0: 39 $uniq
44 $uniq 40 #end if
45 #end if 41 #end if
46 #end if 42 $uniq_start
47 $uniq_start 43 #if $mismatch:
48 #if $mismatch: 44 -mismatch $mismatch
49 -mismatch $mismatch 45 #end if
50 #end if 46 $nosecondary
51 $nosecondary 47 $noqcfail
52 $noqcfail 48 $nopcrdup
53 $nopcrdup 49 #if $excludebed:
54 #if $excludebed: 50 -excludebed ${excludebed} $ignore_strand
55 -excludebed ${excludebed} $ignore_strand 51 #end if
56 #end if 52 #if $includebed:
57 #if $includebed: 53 -includebed ${includebed} $ignore_strand
58 -includebed ${includebed} $ignore_strand 54 #end if
59 #end if 55 #if $includeref:
60 #if $includeref: 56 -includeref ${includeref}
61 -includeref ${includeref} 57 #end if
62 #end if 58 #if $excluderef:
63 #if $excluderef: 59 -excluderef ${excluderef}
64 -excluderef ${excluderef} 60 #end if
65 #end if 61 #if $maximum_mismatch_ratio
66 #if $maximum_mismatch_ratio 62 -maximum_mismatch_ratio $maximum_mismatch_ratio
67 -maximum_mismatch_ratio $maximum_mismatch_ratio 63 #end if
68 #end if 64 ]]></configfile>
69 ]]>
70 </configfile>
71 </configfiles> 65 </configfiles>
72 <inputs> 66 <inputs>
73 <param name="infile" type="data" format="bam" label="Select BAM dataset" /> 67 <param name="infile" type="data" format="bam" label="Select BAM dataset" />
74 <param argument="-minlen" type="integer" value="" optional="True" min="0" 68 <param argument="-minlen" type="integer" value="" optional="True" min="0"
75 label="Remove reads that are smaller than" 69 label="Remove reads that are smaller than"
127 help="e.g. chrM, or _dup chromosomes" /> 121 help="e.g. chrM, or _dup chromosomes" />
128 122
129 <param argument="-maximum_mismatch_ratio" type="float" value="" optional="True" min="0.0" max="1.0" 123 <param argument="-maximum_mismatch_ratio" type="float" value="" optional="True" min="0.0" max="1.0"
130 label="Filter by maximum mismatch ratio" 124 label="Filter by maximum mismatch ratio"
131 help="fraction of length"/> 125 help="fraction of length"/>
132
133 </inputs> 126 </inputs>
134 <outputs> 127 <outputs>
135 <data format="bam" name="outfile" /> 128 <data format="bam" name="outfile" />
136 </outputs> 129 </outputs>
137 <tests> 130 <tests>
232 | -includeref refname | Exclude reads NOT mapped to a reference | 225 | -includeref refname | Exclude reads NOT mapped to a reference |
233 +--------------------------------+-------------------------------------------------+ 226 +--------------------------------+-------------------------------------------------+
234 | -excluderef refname | Exclude reads mapped to a particular reference | 227 | -excluderef refname | Exclude reads mapped to a particular reference |
235 | | (e.g. chrM, or _dup chromosomes) | 228 | | (e.g. chrM, or _dup chromosomes) |
236 +--------------------------------+-------------------------------------------------+ 229 +--------------------------------+-------------------------------------------------+
237 ]]> 230 ]]></help>
238 </help>
239 </tool> 231 </tool>