Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/IntervalToBed.xml @ 25:b43c420a6135 draft default tip
Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
author | timpalpant |
---|---|
date | Sat, 09 Feb 2019 14:02:24 -0500 |
parents | 9d56b5b85740 |
children |
rev | line source |
---|---|
20
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
1 <tool id="IntervalToBed" name="SAM/BAM/GFF/BedGraph/BigBed/VCF to Bed" version="1.0.0"> |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
2 <description>converter</description> |
25
b43c420a6135
Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
timpalpant
parents:
20
diff
changeset
|
3 <command interpreter="bash">galaxyToolRunner.sh converters.IntervalToBed -i $input -o $output</command> |
20
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
4 <inputs> |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
5 <param name="input" type="data" format="sam,bam,gff,bigbed,bedgraph,vcf" label="Input" /> |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
6 </inputs> |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
7 <outputs> |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
8 <data name="output" format="bed" metadata_source="input" /> |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
9 </outputs> |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
10 <help> |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
11 |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
12 This tool will convert any file in SAM, BAM, GFF, BedGraph, BigBed, or VCF format to Bed format. |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
13 |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
14 .. class:: warningmark |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
15 |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
16 For SAM/BAM data, paired-end reads are converted to Bed format as the entire fragment (5' end of mate 1 to the 5' end of mate 2). Single-end reads are converted to Bed format as the read itself, with strand information. If your SAM/BAM file contains both mate alignments from a paired-end sequencing run (i.e. two entries for each fragment), you should first filter out reads from either the + or - strand with the SAM Tools -> Filter SAM tool to avoid producing redundant entries in the output Bed file. |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
17 |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
18 </help> |
9d56b5b85740
Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff
changeset
|
19 </tool> |