Mercurial > repos > devteam > samtool_filter2
comparison samtool_filter2.xml @ 18:a201937caf2e draft
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"/> |