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comparison samtool_filter2.xml @ 18:a201937caf2e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6
author iuc
date Wed, 31 Jul 2019 14:19:38 -0400
parents 3263a2b5d9f0
children
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17:3263a2b5d9f0 18:a201937caf2e
1 <tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.8"> 1 <tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.8+galaxy1">
2 <description>files on FLAG MAPQ RG LN or by region</description> 2 <description>files on FLAG MAPQ RG LN or by region</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.8">samtools</requirement> 4 <requirement type="package" version="1.8">samtools</requirement>
5 </requirements> 5 </requirements>
6 <macros>
7 <xml name="flag_options">
8 <option value="0x0001">Read is paired</option>
9 <option value="0x0002">Read is mapped in a proper pair</option>
10 <option value="0x0004">The read is unmapped</option>
11 <option value="0x0008">The mate is unmapped</option>
12 <option value="0x0010">Read is mapped to the reverse strand of the reference</option>
13 <option value="0x0020">Mate is mapped to the reverse strand of the reference</option>
14 <option value="0x0040">Read is the first in a pair</option>
15 <option value="0x0080">Read is the second in a pair</option>
16 <option value="0x0100">The alignment of this read is not primary</option>
17 <option value="0x0200">The read fails platform/vendor quality checks</option>
18 <option value="0x0400">The read is a PCR or optical duplicate</option>
19 <option value="0x0800">Supplementary alignment</option>
20 </xml>
21 </macros>
6 <command detect_errors="exit_code"><![CDATA[ 22 <command detect_errors="exit_code"><![CDATA[
7 ##set up input files, regions requires input.bam and input.bai 23 ##set up input files, regions requires input.bam and input.bai
8 #if $input1.is_of_type('bam') 24 #if $input1.is_of_type('bam')
9 #set $input = 'input.bam' 25 #set $input = 'input.bam'
10 ln -s '$input1' $input && 26 ln -s '$input1' $input &&
76 <option value="yes">yes</option> 92 <option value="yes">yes</option>
77 </param> 93 </param>
78 <when value="no"/> 94 <when value="no"/>
79 <when value="yes"> 95 <when value="yes">
80 <param name="reqBits" type="select" multiple="true" display="checkboxes" label="Only output alignments with all of these flag bits set" help="(-f)"> 96 <param name="reqBits" type="select" multiple="true" display="checkboxes" label="Only output alignments with all of these flag bits set" help="(-f)">
81 <option value="0x0001">Read is paired</option> 97 <expand macro="flag_options" />
82 <option value="0x0002">Read is mapped in a proper pair</option>
83 <option value="0x0004">The read is unmapped</option>
84 <option value="0x0008">The mate is unmapped</option>
85 <option value="0x0010">Read strand</option>
86 <option value="0x0020">Mate strand</option>
87 <option value="0x0040">Read is the first in a pair</option>
88 <option value="0x0080">Read is the second in a pair</option>
89 <option value="0x0100">The alignment or this read is not primary</option>
90 <option value="0x0200">The read fails platform/vendor quality checks</option>
91 <option value="0x0400">The read is a PCR or optical duplicate</option>
92 <option value="0x0800">Supplementary alignment</option>
93 </param> 98 </param>
94 <param name="skipBits" type="select" multiple="true" display="checkboxes" label="Skip alignments with any of these flag bits set" help="(-F)"> 99 <param name="skipBits" type="select" multiple="true" display="checkboxes" label="Skip alignments with any of these flag bits set" help="(-F)">
95 <option value="0x0001">Read is paired</option> 100 <expand macro="flag_options" />
96 <option value="0x0002">Read is mapped in a proper pair</option>
97 <option value="0x0004">The read is unmapped</option>
98 <option value="0x0008">The mate is unmapped</option>
99 <option value="0x0010">Read strand</option>
100 <option value="0x0020">Mate strand</option>
101 <option value="0x0040">Read is the first in a pair</option>
102 <option value="0x0080">Read is the second in a pair</option>
103 <option value="0x0100">The alignment or this read is not primary</option>
104 <option value="0x0200">The read fails platform/vendor quality checks</option>
105 <option value="0x0400">The read is a PCR or optical duplicate</option>
106 <option value="0x0800">Supplementary alignment</option>
107 </param> 101 </param>
108 </when> 102 </when>
109 </conditional> 103 </conditional>
110 <param name="library" type="text" value="" label="Select alignments from Library" 104 <param name="library" type="text" value="" label="Select alignments from Library"
111 help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/> 105 help="(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/>