| Previous changeset 7:56c31114ad4a (2018-06-06) Next changeset 9:649a225999a5 (2019-11-24) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samtool_filter2 commit 2a605a22c4cb4b537644904d4ef74204ac9865e6 |
|
modified:
samtool_filter2.xml |
| b |
| diff -r 56c31114ad4a -r a7add3e93cc5 samtool_filter2.xml --- a/samtool_filter2.xml Wed Jun 06 18:43:29 2018 -0400 +++ b/samtool_filter2.xml Wed Jul 31 14:19:58 2019 -0400 |
| [ |
| @@ -1,8 +1,24 @@ -<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.8"> +<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.8+galaxy1"> <description>files on FLAG MAPQ RG LN or by region</description> <requirements> <requirement type="package" version="1.8">samtools</requirement> </requirements> + <macros> + <xml name="flag_options"> + <option value="0x0001">Read is paired</option> + <option value="0x0002">Read is mapped in a proper pair</option> + <option value="0x0004">The read is unmapped</option> + <option value="0x0008">The mate is unmapped</option> + <option value="0x0010">Read is mapped to the reverse strand of the reference</option> + <option value="0x0020">Mate is mapped to the reverse strand of the reference</option> + <option value="0x0040">Read is the first in a pair</option> + <option value="0x0080">Read is the second in a pair</option> + <option value="0x0100">The alignment of this read is not primary</option> + <option value="0x0200">The read fails platform/vendor quality checks</option> + <option value="0x0400">The read is a PCR or optical duplicate</option> + <option value="0x0800">Supplementary alignment</option> + </xml> + </macros> <command detect_errors="exit_code"><![CDATA[ ##set up input files, regions requires input.bam and input.bai #if $input1.is_of_type('bam') @@ -78,32 +94,10 @@ <when value="no"/> <when value="yes"> <param name="reqBits" type="select" multiple="true" display="checkboxes" label="Only output alignments with all of these flag bits set" help="(-f)"> - <option value="0x0001">Read is paired</option> - <option value="0x0002">Read is mapped in a proper pair</option> - <option value="0x0004">The read is unmapped</option> - <option value="0x0008">The mate is unmapped</option> - <option value="0x0010">Read strand</option> - <option value="0x0020">Mate strand</option> - <option value="0x0040">Read is the first in a pair</option> - <option value="0x0080">Read is the second in a pair</option> - <option value="0x0100">The alignment or this read is not primary</option> - <option value="0x0200">The read fails platform/vendor quality checks</option> - <option value="0x0400">The read is a PCR or optical duplicate</option> - <option value="0x0800">Supplementary alignment</option> + <expand macro="flag_options" /> </param> <param name="skipBits" type="select" multiple="true" display="checkboxes" label="Skip alignments with any of these flag bits set" help="(-F)"> - <option value="0x0001">Read is paired</option> - <option value="0x0002">Read is mapped in a proper pair</option> - <option value="0x0004">The read is unmapped</option> - <option value="0x0008">The mate is unmapped</option> - <option value="0x0010">Read strand</option> - <option value="0x0020">Mate strand</option> - <option value="0x0040">Read is the first in a pair</option> - <option value="0x0080">Read is the second in a pair</option> - <option value="0x0100">The alignment or this read is not primary</option> - <option value="0x0200">The read fails platform/vendor quality checks</option> - <option value="0x0400">The read is a PCR or optical duplicate</option> - <option value="0x0800">Supplementary alignment</option> + <expand macro="flag_options" /> </param> </when> </conditional> |